diff --git a/eng/common/pipelines/codeowners-linter.yml b/eng/common/pipelines/codeowners-linter.yml
index 56d617d6051a..c1ee612a0999 100644
--- a/eng/common/pipelines/codeowners-linter.yml
+++ b/eng/common/pipelines/codeowners-linter.yml
@@ -21,6 +21,7 @@ stages:
   variables:
     skipComponentGovernanceDetection: true
     nugetMultiFeedWarnLevel: 'none'
+    baseBranchBaseline: ''
 
   jobs:
   - job: Run
@@ -30,21 +31,13 @@ stages:
       vmImage: ubuntu-22.04
 
     variables:
-      CodeownersLinterVersion: '1.0.0-dev.20240227.2'
+      CodeownersLinterVersion: '1.0.0-dev.20240514.2'
       DotNetDevOpsFeed: "https://pkgs.dev.azure.com/azure-sdk/public/_packaging/azure-sdk-for-net/nuget/v3/index.json"
       RepoLabelUri: "https://azuresdkartifacts.blob.core.windows.net/azure-sdk-write-teams/repository-labels-blob"
       TeamUserUri: "https://azuresdkartifacts.blob.core.windows.net/azure-sdk-write-teams/azure-sdk-write-teams-blob"
       UserOrgUri: "https://azuresdkartifacts.blob.core.windows.net/azure-sdk-write-teams/user-org-visibility-blob"
 
     steps:
-      # Skip sparse checkout for the `azure-sdk-for-<lang>-pr` private mirrored repositories
-      # as we require the github service connection to be loaded.
-      - ${{ if not(contains(variables['Build.DefinitionName'], '-pr - ')) }}:
-        - template: /eng/common/pipelines/templates/steps/sparse-checkout.yml
-          parameters:
-            Paths:
-              - '/*'
-
       - task: DotNetCoreCLI@2
         displayName: 'Install CodeownersLinter'
         inputs:
@@ -52,7 +45,32 @@ stages:
           custom: 'tool'
           arguments: 'install --global --add-source "$(DotNetDevOpsFeed)" --version "$(CodeownersLinterVersion)" "Azure.Sdk.Tools.CodeownersLinter"'
           workingDirectory: '$(Build.SourcesDirectory)/eng/common'
+
+      - ${{ if eq(variables['Build.Reason'], 'PullRequest') }}:
+        - pwsh: |
+            Write-Host "git checkout $ENV:SYSTEM_PULLREQUEST_TARGETBRANCH"
+            git checkout $ENV:SYSTEM_PULLREQUEST_TARGETBRANCH
+          displayName: Checkout the base branch
+
+        - pwsh: |
+            # Generate the base branch baseline file to the Build.BinariesDirectory. This will create
+            # a baseline error file against the CODEOWNERS in the base branch
+            $baseBranchBaselineFile = "$(Build.BinariesDirectory)/CODEOWNERS_BaseBranch_Baseline_errors.txt"
+            Write-Host "codeowners-linter --repoRoot $(Build.SourcesDirectory) --repoName $(Build.Repository.Name) -gbl -rUri ""$(RepoLabelUri)"" -tUri ""$(TeamUserUri)"" -uUri ""$(UserOrgUri)"" -bbf ""$baseBranchBaselineFile"""
+            codeowners-linter --repoRoot $(Build.SourcesDirectory) --repoName $(Build.Repository.Name) -gbl -rUri "$(RepoLabelUri)" -tUri "$(TeamUserUri)" -uUri "$(UserOrgUri)" -bbf "$baseBranchBaselineFile"
+            echo "##vso[task.setvariable variable=baseBranchBaseline]$baseBranchBaselineFile"
+          displayName: 'Generate baseline file for base branch'
+          workingDirectory: '$(Build.SourcesDirectory)/eng/common'
+
+        - pwsh: |
+            Write-Host "git checkout refs/remotes/pull/$ENV:SYSTEM_PULLREQUEST_PULLREQUESTNUMBER/merge"
+            git checkout refs/remotes/pull/$ENV:SYSTEM_PULLREQUEST_PULLREQUESTNUMBER/merge
+          displayName: Checkout the PR branch
+
       - pwsh: |
-          codeowners-linter --repoRoot $(Build.SourcesDirectory) --repoName $(Build.Repository.Name) -fbl -rUri "$(RepoLabelUri)" -tUri "$(TeamUserUri)" -uUri "$(UserOrgUri)"
+          # In the case of a PR, the baseBranchBaseline will be set which will be used to further filter results.
+          # For scheduled runs, the baseBranchBaseline won't be set and only the existing baseline file will be used to filter
+          Write-Host "codeowners-linter --repoRoot $(Build.SourcesDirectory) --repoName $(Build.Repository.Name) -fbl -rUri ""$(RepoLabelUri)"" -tUri ""$(TeamUserUri)"" -uUri ""$(UserOrgUri)"" -bbf ""$(baseBranchBaseline)"""
+          codeowners-linter --repoRoot $(Build.SourcesDirectory) --repoName $(Build.Repository.Name) -fbl -rUri "$(RepoLabelUri)" -tUri "$(TeamUserUri)" -uUri "$(UserOrgUri)" -bbf "$(baseBranchBaseline)"
         displayName: 'Lint CODEOWNERS and filter using baseline'
         workingDirectory: '$(Build.SourcesDirectory)/eng/common'