diff --git a/Sources/CoreCommands/SwiftToolObservabilityHandler.swift b/Sources/CoreCommands/SwiftToolObservabilityHandler.swift
index 1bbbadd4010..f8958b45e1e 100644
--- a/Sources/CoreCommands/SwiftToolObservabilityHandler.swift
+++ b/Sources/CoreCommands/SwiftToolObservabilityHandler.swift
@@ -53,7 +53,7 @@ public struct SwiftToolObservabilityHandler: ObservabilityHandlerProvider {
         self.outputHandler.prompt(message: message, completion: completion)
     }
 
-    func wait(timeout: DispatchTime) {
+    public func wait(timeout: DispatchTime) {
         self.outputHandler.wait(timeout: timeout)
     }
 
@@ -212,12 +212,3 @@ extension Basics.Diagnostic.Severity {
         return self <= .info
     }
 }
-
-extension ObservabilitySystem {
-    public static func swiftTool(
-        outputStream: OutputByteStream = stdoutStream,
-        logLevel: Basics.Diagnostic.Severity = .warning
-    ) -> ObservabilitySystem {
-        .init(SwiftToolObservabilityHandler(outputStream: stdoutStream, logLevel: logLevel))
-    }
-}
diff --git a/Sources/CrossCompilationDestinationsTool/CMakeLists.txt b/Sources/CrossCompilationDestinationsTool/CMakeLists.txt
index 7352b02e833..a15558c575b 100644
--- a/Sources/CrossCompilationDestinationsTool/CMakeLists.txt
+++ b/Sources/CrossCompilationDestinationsTool/CMakeLists.txt
@@ -7,6 +7,9 @@
 # See http://swift.org/CONTRIBUTORS.txt for Swift project authors
 
 add_library(CrossCompilationDestinationsTool
+  Configuration/ConfigureDestination.swift
+  Configuration/ResetConfiguration.swift
+  Configuration/ShowConfiguration.swift
   DestinationCommand.swift
   InstallDestination.swift
   ListDestinations.swift
diff --git a/Sources/CrossCompilationDestinationsTool/Configuration/ConfigureDestination.swift b/Sources/CrossCompilationDestinationsTool/Configuration/ConfigureDestination.swift
new file mode 100644
index 00000000000..abdabc996ac
--- /dev/null
+++ b/Sources/CrossCompilationDestinationsTool/Configuration/ConfigureDestination.swift
@@ -0,0 +1,26 @@
+//===----------------------------------------------------------------------===//
+//
+// This source file is part of the Swift open source project
+//
+// Copyright (c) 2023 Apple Inc. and the Swift project authors
+// Licensed under Apache License v2.0 with Runtime Library Exception
+//
+// See http://swift.org/LICENSE.txt for license information
+// See http://swift.org/CONTRIBUTORS.txt for the list of Swift project authors
+//
+//===----------------------------------------------------------------------===//
+
+import ArgumentParser
+
+struct ConfigureDestination: ParsableCommand {
+    static let configuration = CommandConfiguration(
+        commandName: "configuration",
+        abstract: """
+        Manages configuration options for installed cross-compilation destinations.
+        """,
+        subcommands: [
+            ResetConfiguration.self,
+            ShowConfiguration.self,
+        ]
+    )
+}
diff --git a/Sources/CrossCompilationDestinationsTool/Configuration/ResetConfiguration.swift b/Sources/CrossCompilationDestinationsTool/Configuration/ResetConfiguration.swift
new file mode 100644
index 00000000000..c3c750bb758
--- /dev/null
+++ b/Sources/CrossCompilationDestinationsTool/Configuration/ResetConfiguration.swift
@@ -0,0 +1,129 @@
+//===----------------------------------------------------------------------===//
+//
+// This source file is part of the Swift open source project
+//
+// Copyright (c) 2023 Apple Inc. and the Swift project authors
+// Licensed under Apache License v2.0 with Runtime Library Exception
+//
+// See http://swift.org/LICENSE.txt for license information
+// See http://swift.org/CONTRIBUTORS.txt for the list of Swift project authors
+//
+//===----------------------------------------------------------------------===//
+
+import ArgumentParser
+import Basics
+import CoreCommands
+import PackageModel
+
+import struct TSCBasic.AbsolutePath
+
+struct ResetConfiguration: DestinationCommand {
+    static let configuration = CommandConfiguration(
+        commandName: "reset",
+        abstract: """
+        Resets configuration properties currently applied to a given destination and run-time triple. If no specific \
+        property is specified, all of them are reset for the destination.
+        """
+    )
+
+    @OptionGroup(visibility: .hidden)
+    var locations: LocationOptions
+
+    @Flag(help: "Reset custom configuration for a path to a directory containing the SDK root.")
+    var sdkRootPath = false
+
+    @Flag(help: "Reset custom configuration for a path to a directory containing Swift resources for dynamic linking.")
+    var swiftResourcesPath = false
+
+    @Flag(help: "Reset custom configuration for a path to a directory containing Swift resources for static linking.")
+    var swiftStaticResourcesPath = false
+
+    @Flag(help: "Reset custom configuration for a path to a directory containing headers.")
+    var includeSearchPath = false
+
+    @Flag(help: "Reset custom configuration for a path to a directory containing libraries.")
+    var librarySearchPath = false
+
+    @Flag(help: "Reset custom configuration for a path to a toolset file.")
+    var toolsetPath = false
+
+    @Argument(
+        help: """
+        An identifier of an already installed destination. Use the `list` subcommand to see all available \
+        identifiers.
+        """
+    )
+    var destinationID: String
+
+    @Argument(help: "The run-time triple of the destination to configure.")
+    var runTimeTriple: String
+
+    func run(
+        buildTimeTriple: Triple,
+        _ destinationsDirectory: AbsolutePath,
+        _ observabilityScope: ObservabilityScope
+    ) throws {
+        let configurationStore = try DestinationConfigurationStore(
+            buildTimeTriple: buildTimeTriple,
+            destinationsDirectoryPath: destinationsDirectory,
+            fileSystem: fileSystem,
+            observabilityScope: observabilityScope
+        )
+
+        let triple = try Triple(runTimeTriple)
+
+        guard var destination = try configurationStore.readConfiguration(
+            destinationID: destinationID,
+            runTimeTriple: triple
+        ) else {
+            throw DestinationError.destinationNotFound(
+                artifactID: destinationID,
+                builtTimeTriple: buildTimeTriple,
+                runTimeTriple: triple
+            )
+        }
+
+        var configuration = destination.pathsConfiguration
+        var shouldResetAll = true
+
+        if sdkRootPath {
+            configuration.sdkRootPath = nil
+            shouldResetAll = false
+        }
+
+        if swiftResourcesPath {
+            configuration.swiftResourcesPath = nil
+            shouldResetAll = false
+        }
+
+        if swiftStaticResourcesPath {
+            configuration.swiftResourcesPath = nil
+            shouldResetAll = false
+        }
+
+        if includeSearchPath {
+            configuration.includeSearchPaths = nil
+            shouldResetAll = false
+        }
+
+        if librarySearchPath {
+            configuration.librarySearchPaths = nil
+            shouldResetAll = false
+        }
+
+        if toolsetPath {
+            configuration.toolsetPaths = nil
+            shouldResetAll = false
+        }
+
+        if shouldResetAll {
+            if try !configurationStore.resetConfiguration(destinationID: destinationID, runTimeTriple: triple) {
+                observabilityScope.emit(
+                    warning: "No configuration for destination \(destinationID)"
+                )
+            }
+        } else {
+            try configurationStore.updateConfiguration(destinationID: destinationID, destination: destination)
+        }
+    }
+}
diff --git a/Sources/CrossCompilationDestinationsTool/Configuration/ShowConfiguration.swift b/Sources/CrossCompilationDestinationsTool/Configuration/ShowConfiguration.swift
new file mode 100644
index 00000000000..f59cb2d9ee7
--- /dev/null
+++ b/Sources/CrossCompilationDestinationsTool/Configuration/ShowConfiguration.swift
@@ -0,0 +1,94 @@
+//===----------------------------------------------------------------------===//
+//
+// This source file is part of the Swift open source project
+//
+// Copyright (c) 2023 Apple Inc. and the Swift project authors
+// Licensed under Apache License v2.0 with Runtime Library Exception
+//
+// See http://swift.org/LICENSE.txt for license information
+// See http://swift.org/CONTRIBUTORS.txt for the list of Swift project authors
+//
+//===----------------------------------------------------------------------===//
+
+import ArgumentParser
+import Basics
+import CoreCommands
+import PackageModel
+
+import struct TSCBasic.AbsolutePath
+
+struct ShowConfiguration: DestinationCommand {
+    static let configuration = CommandConfiguration(
+        commandName: "show",
+        abstract: """
+        Prints all configuration properties currently applied to a given destination and run-time triple.
+        """
+    )
+
+    @OptionGroup(visibility: .hidden)
+    var locations: LocationOptions
+
+    @Argument(
+        help: """
+        An identifier of an already installed destination. Use the `list` subcommand to see all available \
+        identifiers.
+        """
+    )
+    var destinationID: String
+
+    @Argument(help: "The run-time triple of the destination to configure.")
+    var runTimeTriple: String
+
+    func run(
+        buildTimeTriple: Triple,
+        _ destinationsDirectory: AbsolutePath,
+        _ observabilityScope: ObservabilityScope
+    ) throws {
+        let configurationStore = try DestinationConfigurationStore(
+            buildTimeTriple: buildTimeTriple,
+            destinationsDirectoryPath: destinationsDirectory,
+            fileSystem: fileSystem,
+            observabilityScope: observabilityScope
+        )
+
+        let triple = try Triple(runTimeTriple)
+
+        guard let configuration = try configurationStore.readConfiguration(
+            destinationID: destinationID,
+            runTimeTriple: triple
+        )?.pathsConfiguration else {
+            throw DestinationError.destinationNotFound(
+                artifactID: destinationID,
+                builtTimeTriple: buildTimeTriple,
+                runTimeTriple: triple
+            )
+        }
+
+        print(configuration)
+    }
+}
+
+extension Destination.PathsConfiguration: CustomStringConvertible {
+    public var description: String {
+        """
+        sdkRootPath: \(sdkRootPath.configurationString)
+        swiftResourcesPath: \(swiftResourcesPath.configurationString)
+        swiftStaticResourcesPath: \(swiftStaticResourcesPath.configurationString)
+        includeSearchPaths: \(includeSearchPaths.configurationString)
+        librarySearchPaths: \(librarySearchPaths.configurationString)
+        toolsetPaths: \(toolsetPaths.configurationString)
+        """
+    }
+}
+
+extension Optional where Wrapped == AbsolutePath {
+    fileprivate var configurationString: String {
+        self?.pathString ?? "not set"
+    }
+}
+
+extension Optional where Wrapped == [AbsolutePath] {
+    fileprivate var configurationString: String {
+        self?.map(\.pathString).description ?? "not set"
+    }
+}
diff --git a/Sources/CrossCompilationDestinationsTool/DestinationCommand.swift b/Sources/CrossCompilationDestinationsTool/DestinationCommand.swift
index 212be0f3e2c..5451927a5cf 100644
--- a/Sources/CrossCompilationDestinationsTool/DestinationCommand.swift
+++ b/Sources/CrossCompilationDestinationsTool/DestinationCommand.swift
@@ -11,13 +11,31 @@
 //===----------------------------------------------------------------------===//
 
 import ArgumentParser
+import Basics
 import CoreCommands
-import TSCBasic
+import Dispatch
+import PackageModel
+
+import struct TSCBasic.AbsolutePath
+import protocol TSCBasic.FileSystem
+import var TSCBasic.localFileSystem
+import var TSCBasic.stdoutStream
 
 /// A protocol for functions and properties common to all destination subcommands.
 protocol DestinationCommand: ParsableCommand {
     /// Common locations options provided by ArgumentParser.
     var locations: LocationOptions { get }
+
+    /// Run a command operating on cross-compilation destinations, passing it required configuration values.
+    /// - Parameters:
+    ///   - buildTimeTriple: triple of the machine this command is running on.
+    ///   - destinationsDirectory: directory containing destination artifact bundles and their configuration.
+    ///   - observabilityScope: observability scope used for logging.
+    func run(
+        buildTimeTriple: Triple,
+        _ destinationsDirectory: AbsolutePath,
+        _ observabilityScope: ObservabilityScope
+    ) throws
 }
 
 extension DestinationCommand {
@@ -43,4 +61,31 @@ extension DestinationCommand {
 
         return destinationsDirectory
     }
+
+    public func run() throws {
+        let observabilityHandler = SwiftToolObservabilityHandler(outputStream: stdoutStream, logLevel: .info)
+        let observabilitySystem = ObservabilitySystem(observabilityHandler)
+        let observabilityScope = observabilitySystem.topScope
+        let destinationsDirectory = try self.getOrCreateDestinationsDirectory()
+
+        let hostToolchain = try UserToolchain(destination: Destination.hostDestination())
+        let triple = Triple.getHostTriple(usingSwiftCompiler: hostToolchain.swiftCompilerPath)
+
+        var commandError: Error? = nil
+        do {
+            try self.run(buildTimeTriple: triple, destinationsDirectory, observabilityScope)
+            if observabilityScope.errorsReported {
+                throw ExitCode.failure
+            }
+        } catch {
+            commandError = error
+        }
+
+        // wait for all observability items to process
+        observabilityHandler.wait(timeout: .now() + 5)
+
+        if let error = commandError {
+            throw error
+        }
+    }
 }
diff --git a/Sources/CrossCompilationDestinationsTool/InstallDestination.swift b/Sources/CrossCompilationDestinationsTool/InstallDestination.swift
index 797622b4a8c..ec3fe5378f5 100644
--- a/Sources/CrossCompilationDestinationsTool/InstallDestination.swift
+++ b/Sources/CrossCompilationDestinationsTool/InstallDestination.swift
@@ -35,11 +35,11 @@ struct InstallDestination: DestinationCommand {
     @Argument(help: "A local filesystem path or a URL of an artifact bundle to install.")
     var bundlePathOrURL: String
 
-    func run() throws {
-        let observabilitySystem = ObservabilitySystem.swiftTool()
-        let observabilityScope = observabilitySystem.topScope
-        let destinationsDirectory = try self.getOrCreateDestinationsDirectory()
-
+    func run(
+        buildTimeTriple: Triple,
+        _ destinationsDirectory: AbsolutePath,
+        _ observabilityScope: ObservabilityScope
+    ) throws {
         if
             let bundleURL = URL(string: bundlePathOrURL),
             let scheme = bundleURL.scheme,
@@ -78,6 +78,6 @@ struct InstallDestination: DestinationCommand {
             throw StringError("Argument `\(bundlePathOrURL)` is neither a valid filesystem path nor a URL.")
         }
 
-        print("Destination artifact bundle at `\(bundlePathOrURL)` successfully installed.")
+        observabilityScope.emit(info: "Destination artifact bundle at `\(bundlePathOrURL)` successfully installed.")
     }
 }
diff --git a/Sources/CrossCompilationDestinationsTool/ListDestinations.swift b/Sources/CrossCompilationDestinationsTool/ListDestinations.swift
index 6accc860a92..cbf5e91d18f 100644
--- a/Sources/CrossCompilationDestinationsTool/ListDestinations.swift
+++ b/Sources/CrossCompilationDestinationsTool/ListDestinations.swift
@@ -15,9 +15,10 @@ import Basics
 import CoreCommands
 import PackageModel
 import SPMBuildCore
-import TSCBasic
 
-public struct ListDestinations: DestinationCommand {
+import struct TSCBasic.AbsolutePath
+
+struct ListDestinations: DestinationCommand {
     public static let configuration = CommandConfiguration(
         commandName: "list",
         abstract:
@@ -29,13 +30,11 @@ public struct ListDestinations: DestinationCommand {
     @OptionGroup()
     var locations: LocationOptions
 
-    public init() {}
-
-    public func run() throws {
-        let observabilitySystem = ObservabilitySystem.swiftTool()
-        let observabilityScope = observabilitySystem.topScope
-        let destinationsDirectory = try self.getOrCreateDestinationsDirectory()
-
+    func run(
+        buildTimeTriple: Triple,
+        _ destinationsDirectory: AbsolutePath,
+        _ observabilityScope: ObservabilityScope
+    ) throws {
         let validBundles = try DestinationBundle.getAllValidBundles(
             destinationsDirectory: destinationsDirectory,
             fileSystem: fileSystem,
@@ -43,7 +42,7 @@ public struct ListDestinations: DestinationCommand {
         )
 
         guard !validBundles.isEmpty else {
-            print("No cross-compilation destinations are currently installed.")
+            observabilityScope.emit(info: "No cross-compilation destinations are currently installed.")
             return
         }
 
diff --git a/Sources/CrossCompilationDestinationsTool/RemoveDestination.swift b/Sources/CrossCompilationDestinationsTool/RemoveDestination.swift
index e6a250ba495..cf3aa60072a 100644
--- a/Sources/CrossCompilationDestinationsTool/RemoveDestination.swift
+++ b/Sources/CrossCompilationDestinationsTool/RemoveDestination.swift
@@ -14,6 +14,8 @@ import ArgumentParser
 import Basics
 import CoreCommands
 
+import struct TSCBasic.AbsolutePath
+
 struct RemoveDestination: DestinationCommand {
     static let configuration = CommandConfiguration(
         commandName: "remove",
@@ -28,7 +30,11 @@ struct RemoveDestination: DestinationCommand {
     @Argument(help: "Name of the destination artifact bundle to remove from the filesystem.")
     var bundleName: String
 
-    func run() throws {
+    func run(
+        buildTimeTriple: Triple,
+        _ destinationsDirectory: AbsolutePath,
+        _ observabilityScope: ObservabilityScope
+    ) throws {
         let destinationsDirectory = try self.getOrCreateDestinationsDirectory()
         let artifactBundleDirectory = destinationsDirectory.appending(component: self.bundleName)
 
diff --git a/Sources/CrossCompilationDestinationsTool/SwiftDestinationTool.swift b/Sources/CrossCompilationDestinationsTool/SwiftDestinationTool.swift
index 464bb1bba51..c54ed44c899 100644
--- a/Sources/CrossCompilationDestinationsTool/SwiftDestinationTool.swift
+++ b/Sources/CrossCompilationDestinationsTool/SwiftDestinationTool.swift
@@ -20,6 +20,7 @@ public struct SwiftDestinationTool: ParsableCommand {
         abstract: "Perform operations on Swift cross-compilation destinations.",
         version: SwiftVersion.current.completeDisplayString,
         subcommands: [
+            ConfigureDestination.self,
             InstallDestination.self,
             ListDestinations.self,
             RemoveDestination.self,
diff --git a/Sources/PackageModel/Destination.swift b/Sources/PackageModel/Destination.swift
index 01677e7da32..36040cba781 100644
--- a/Sources/PackageModel/Destination.swift
+++ b/Sources/PackageModel/Destination.swift
@@ -176,19 +176,91 @@ public struct Destination: Equatable {
         public var sdkRootPath: AbsolutePath?
 
         /// Path containing Swift resources for dynamic linking.
-        private(set) var swiftResourcesPath: AbsolutePath?
+        public var swiftResourcesPath: AbsolutePath?
 
         /// Path containing Swift resources for static linking.
-        private(set) var swiftStaticResourcesPath: AbsolutePath?
+        public var swiftStaticResourcesPath: AbsolutePath?
 
         /// Array of paths containing headers.
-        private(set) var includeSearchPaths: [AbsolutePath]?
+        public var includeSearchPaths: [AbsolutePath]?
 
         /// Array of paths containing libraries.
-        private(set) var librarySearchPaths: [AbsolutePath]?
+        public var librarySearchPaths: [AbsolutePath]?
 
         /// Array of paths containing toolset files.
-        private(set) var toolsetPaths: [AbsolutePath]?
+        public var toolsetPaths: [AbsolutePath]?
+
+        /// Initialize paths configuration from values deserialized using v3 schema.
+        /// - Parameters:
+        ///   - properties: properties of the destination for the given triple.
+        ///   - destinationDirectory: directory used for converting relative paths in `properties` to absolute paths.
+        init(_ properties: SerializedDestinationV3.TripleProperties, destinationDirectory: AbsolutePath? = nil) throws {
+            if let destinationDirectory = destinationDirectory {
+                self.init(
+                    sdkRootPath: try AbsolutePath(validating: properties.sdkRootPath, relativeTo: destinationDirectory),
+                    swiftResourcesPath: try properties.swiftResourcesPath.map {
+                        try AbsolutePath(validating: $0, relativeTo: destinationDirectory)
+                    },
+                    swiftStaticResourcesPath: try properties.swiftStaticResourcesPath.map {
+                        try AbsolutePath(validating: $0, relativeTo: destinationDirectory)
+                    },
+                    includeSearchPaths: try properties.includeSearchPaths?.map {
+                        try AbsolutePath(validating: $0, relativeTo: destinationDirectory)
+                    },
+                    librarySearchPaths: try properties.librarySearchPaths?.map {
+                        try AbsolutePath(validating: $0, relativeTo: destinationDirectory)
+                    },
+                    toolsetPaths: try properties.toolsetPaths?.map {
+                        try AbsolutePath(validating: $0, relativeTo: destinationDirectory)
+                    }
+                )
+            } else {
+                self.init(
+                    sdkRootPath: try AbsolutePath(validating: properties.sdkRootPath),
+                    swiftResourcesPath: try properties.swiftResourcesPath.map {
+                        try AbsolutePath(validating: $0)
+                    },
+                    swiftStaticResourcesPath: try properties.swiftStaticResourcesPath.map {
+                        try AbsolutePath(validating: $0)
+                    },
+                    includeSearchPaths: try properties.includeSearchPaths?.map {
+                        try AbsolutePath(validating: $0)
+                    },
+                    librarySearchPaths: try properties.librarySearchPaths?.map {
+                        try AbsolutePath(validating: $0)
+                    },
+                    toolsetPaths: try properties.toolsetPaths?.map {
+                        try AbsolutePath(validating: $0)
+                    }
+                )
+            }
+        }
+
+        public mutating func merge(with newConfiguration: Self) {
+            if let sdkRootPath = newConfiguration.sdkRootPath {
+                self.sdkRootPath = sdkRootPath
+            }
+
+            if let swiftResourcesPath = newConfiguration.swiftResourcesPath {
+                self.swiftResourcesPath = swiftResourcesPath
+            }
+
+            if let swiftStaticResourcesPath = newConfiguration.swiftStaticResourcesPath {
+                self.swiftStaticResourcesPath = swiftStaticResourcesPath
+            }
+
+            if let includeSearchPaths = newConfiguration.includeSearchPaths {
+                self.includeSearchPaths = includeSearchPaths
+            }
+
+            if let librarySearchPaths = newConfiguration.librarySearchPaths {
+                self.librarySearchPaths = librarySearchPaths
+            }
+
+            if let toolsetPaths = newConfiguration.toolsetPaths {
+                self.toolsetPaths = toolsetPaths
+            }
+        }
     }
 
     /// Configuration of file system paths used by this destination when building.
@@ -469,53 +541,11 @@ extension Destination {
         toolset: Toolset = .init(),
         destinationDirectory: AbsolutePath? = nil
     ) throws {
-        if let destinationDirectory = destinationDirectory {
-            self.init(
-                targetTriple: runTimeTriple,
-                toolset: toolset,
-                pathsConfiguration: .init(
-                    sdkRootPath: try AbsolutePath(validating: properties.sdkRootPath, relativeTo: destinationDirectory),
-                    swiftResourcesPath: try properties.swiftResourcesPath.map {
-                        try AbsolutePath(validating: $0, relativeTo: destinationDirectory)
-                    },
-                    swiftStaticResourcesPath: try properties.swiftStaticResourcesPath.map {
-                        try AbsolutePath(validating: $0, relativeTo: destinationDirectory)
-                    },
-                    includeSearchPaths: try properties.includeSearchPaths?.map {
-                        try AbsolutePath(validating: $0, relativeTo: destinationDirectory)
-                    },
-                    librarySearchPaths: try properties.librarySearchPaths?.map {
-                        try AbsolutePath(validating: $0, relativeTo: destinationDirectory)
-                    },
-                    toolsetPaths: try properties.toolsetPaths?.map {
-                        try AbsolutePath(validating: $0, relativeTo: destinationDirectory)
-                    }
-                )
-            )
-        } else {
-            self.init(
-                targetTriple: runTimeTriple,
-                toolset: toolset,
-                pathsConfiguration: .init(
-                    sdkRootPath: try AbsolutePath(validating: properties.sdkRootPath),
-                    swiftResourcesPath: try properties.swiftResourcesPath.map {
-                        try AbsolutePath(validating: $0)
-                    },
-                    swiftStaticResourcesPath: try properties.swiftStaticResourcesPath.map {
-                        try AbsolutePath(validating: $0)
-                    },
-                    includeSearchPaths: try properties.includeSearchPaths?.map {
-                        try AbsolutePath(validating: $0)
-                    },
-                    librarySearchPaths: try properties.librarySearchPaths?.map {
-                        try AbsolutePath(validating: $0)
-                    },
-                    toolsetPaths: try properties.toolsetPaths?.map {
-                        try AbsolutePath(validating: $0)
-                    }
-                )
-            )
-        }
+        self.init(
+            targetTriple: runTimeTriple,
+            toolset: toolset,
+            pathsConfiguration: try .init(properties, destinationDirectory: destinationDirectory)
+        )
     }
 
     /// Load a ``Destination`` description from a legacy JSON representation from disk.
diff --git a/Sources/PackageModel/DestinationConfigurationStore.swift b/Sources/PackageModel/DestinationConfigurationStore.swift
index 68407a8cfa4..9794e220b24 100644
--- a/Sources/PackageModel/DestinationConfigurationStore.swift
+++ b/Sources/PackageModel/DestinationConfigurationStore.swift
@@ -94,6 +94,20 @@ public final class DestinationConfigurationStore {
             component: "\(destinationID)_\(triple.tripleString).json"
         )
 
+        let destinationBundles = try DestinationBundle.getAllValidBundles(
+            destinationsDirectory: destinationsDirectoryPath,
+            fileSystem: fileSystem,
+            observabilityScope: observabilityScope
+        )
+
+        guard var destination = destinationBundles.selectDestination(
+            id: destinationID,
+            hostTriple: buildTimeTriple,
+            targetTriple: triple
+        ) else {
+            return nil
+        }
+
         if fileSystem.isFile(configurationPath) {
             let properties = try decoder.decode(
                 path: configurationPath,
@@ -101,23 +115,15 @@ public final class DestinationConfigurationStore {
                 as: SerializedDestinationV3.TripleProperties.self
             )
 
-            return try Destination(
-                runTimeTriple: triple,
-                properties: properties
-            )
-        } else {
-            let destinationBundles = try DestinationBundle.getAllValidBundles(
-                destinationsDirectory: destinationsDirectoryPath,
-                fileSystem: fileSystem,
-                observabilityScope: observabilityScope
-            )
-
-            return destinationBundles.selectDestination(
-                id: destinationID,
-                hostTriple: buildTimeTriple,
-                targetTriple: triple
+            destination.pathsConfiguration.merge(
+                with: try Destination(
+                    runTimeTriple: triple,
+                    properties: properties
+                ).pathsConfiguration
             )
         }
+
+        return destination
     }
 
     /// Resets configuration for identified destination triple.