diff --git a/compiler/src/dotty/tools/dotc/semanticdb/ExtractSemanticDB.scala b/compiler/src/dotty/tools/dotc/semanticdb/ExtractSemanticDB.scala
index 071efb1fb91c..84bc1e77a1ef 100644
--- a/compiler/src/dotty/tools/dotc/semanticdb/ExtractSemanticDB.scala
+++ b/compiler/src/dotty/tools/dotc/semanticdb/ExtractSemanticDB.scala
@@ -24,6 +24,7 @@ import scala.annotation.{ threadUnsafe => tu, tailrec }
 import scala.PartialFunction.condOpt
 
 import dotty.tools.dotc.{semanticdb => s}
+import dotty.tools.io.{AbstractFile, JarArchive}
 
 /** Extract symbol references and uses to semanticdb files.
  *  See https://scalameta.org/docs/semanticdb/specification.html#symbol-1
@@ -38,7 +39,9 @@ class ExtractSemanticDB extends Phase:
   override val description: String = ExtractSemanticDB.description
 
   override def isRunnable(using Context) =
-    super.isRunnable && ctx.settings.Xsemanticdb.value
+    import ExtractSemanticDB.{semanticdbTarget, outputDirectory}
+    def writesToOutputJar = semanticdbTarget.isEmpty && outputDirectory.isInstanceOf[JarArchive]
+    super.isRunnable && ctx.settings.Xsemanticdb.value && !writesToOutputJar
 
   // Check not needed since it does not transform trees
   override def isCheckable: Boolean = false
@@ -475,6 +478,13 @@ object ExtractSemanticDB:
   val name: String = "extractSemanticDB"
   val description: String = "extract info into .semanticdb files"
 
+  private def semanticdbTarget(using Context): Option[Path] =
+    Option(ctx.settings.semanticdbTarget.value)
+      .filterNot(_.isEmpty)
+      .map(Paths.get(_))
+
+  private def outputDirectory(using Context): AbstractFile = ctx.settings.outputDir.value
+
   def write(
     source: SourceFile,
     occurrences: List[SymbolOccurrence],
@@ -482,14 +492,8 @@ object ExtractSemanticDB:
     synthetics: List[Synthetic],
   )(using Context): Unit =
     def absolutePath(path: Path): Path = path.toAbsolutePath.normalize
-    val semanticdbTarget =
-      val semanticdbTargetSetting = ctx.settings.semanticdbTarget.value
-      absolutePath(
-        if semanticdbTargetSetting.isEmpty then ctx.settings.outputDir.value.jpath
-        else Paths.get(semanticdbTargetSetting)
-      )
     val relPath = SourceFile.relativePath(source, ctx.settings.sourceroot.value)
-    val outpath = semanticdbTarget
+    val outpath = absolutePath(semanticdbTarget.getOrElse(outputDirectory.jpath))
       .resolve("META-INF")
       .resolve("semanticdb")
       .resolve(relPath)