diff --git a/compiler/src/dotty/tools/dotc/coverage/Coverage.scala b/compiler/src/dotty/tools/dotc/coverage/Coverage.scala
index dde8adcf8659..3c5297334a3b 100644
--- a/compiler/src/dotty/tools/dotc/coverage/Coverage.scala
+++ b/compiler/src/dotty/tools/dotc/coverage/Coverage.scala
@@ -19,11 +19,6 @@ class Coverage:
     if stmt.id >= _nextStatementId then _nextStatementId = stmt.id + 1
     statementsById(stmt.id) = stmt
 
-  def removeStatementsFromFile(sourcePath: Path | Null) =
-    val removedIds = statements.filter(_.location.sourcePath == sourcePath).map(_.id.toLong)
-    removedIds.foreach(statementsById.remove)
-
-
 /**
   * A statement that can be invoked, and thus counted as "covered" by code coverage tools.
   *
diff --git a/compiler/src/dotty/tools/dotc/transform/InstrumentCoverage.scala b/compiler/src/dotty/tools/dotc/transform/InstrumentCoverage.scala
index e0878f34ca22..7528f5c01f57 100644
--- a/compiler/src/dotty/tools/dotc/transform/InstrumentCoverage.scala
+++ b/compiler/src/dotty/tools/dotc/transform/InstrumentCoverage.scala
@@ -2,7 +2,7 @@ package dotty.tools.dotc
 package transform
 
 import java.io.File
-import java.nio.file.Files
+import java.nio.file.{Files, Path}
 
 import ast.tpd.*
 import collection.mutable
@@ -42,54 +42,61 @@ class InstrumentCoverage extends MacroTransform with IdentityDenotTransformer:
 
   private var coverageExcludeClasslikePatterns: List[Pattern] = Nil
   private var coverageExcludeFilePatterns: List[Pattern] = Nil
-  private var lastCompiledFiles: Set[String] = Set.empty
 
-  override def run(using ctx: Context): Unit =
+  override def runOn(units: List[CompilationUnit])(using ctx: Context): List[CompilationUnit] =
     val outputPath = ctx.settings.coverageOutputDir.value
 
-    // Ensure the dir exists
+    // Ensure the dir exists (once per batch, not per unit)
     val dataDir = File(outputPath)
     val newlyCreated = dataDir.mkdirs()
 
     if !newlyCreated then
       // If the directory existed before, clean measurement files.
-      dataDir.listFiles
-        .filter(_.getName.startsWith("scoverage.measurements."))
-        .foreach(_.delete())
+      val files = dataDir.listFiles
+      if files != null then
+        files
+          .filter(_.getName.startsWith("scoverage.measurements."))
+          .foreach(_.delete())
     end if
 
+    // Deserialize previous coverage once at the start
     val coverageFilePath = Serializer.coverageFilePath(outputPath)
     val previousCoverage =
       if Files.exists(coverageFilePath) then
         Serializer.deserialize(coverageFilePath, ctx.settings.sourceroot.value)
       else Coverage()
 
-    // Initialise a coverage object if it does not exist yet
-    if ctx.base.coverage == null then
-      ctx.base.coverage = Coverage()
-
+    // Initialize coverage patterns once
     coverageExcludeClasslikePatterns = ctx.settings.coverageExcludeClasslikes.value.map(_.r.pattern)
     coverageExcludeFilePatterns = ctx.settings.coverageExcludeFiles.value.map(_.r.pattern)
 
-    ctx.base.coverage.nn.removeStatementsFromFile(ctx.compilationUnit.source.file.absolute.jpath)
+    // Initialize coverage object
+    ctx.base.coverage = Coverage()
     ctx.base.coverage.nn.setNextStatementId(previousCoverage.nextStatementId())
 
-    super.run
+    // Run the transformation on all units
+    val result = super.runOn(units)
 
+    // Serialize once at the end with merged coverage
     val mergedCoverage = Coverage()
+    val currentFiles = units.map(_.source.file.absolute.jpath)
 
+    // Add statements from previous coverage that aren't from recompiled files
+    // and whose source files still exist
     previousCoverage.statements
       .filterNot(stmt =>
         val source = stmt.location.sourcePath
-        lastCompiledFiles.contains(source.toString) || !Files.exists(source)
+        currentFiles.contains(source) || !Files.exists(source)
       )
-      .foreach { stmt =>
-        mergedCoverage.addStatement(stmt)
-      }
-    ctx.base.coverage.nn.statements.foreach(stmt => mergedCoverage.addStatement(stmt))
+      .foreach(mergedCoverage.addStatement)
+
+    // Add all new statements from this compilation
+    ctx.base.coverage.nn.statements.foreach(mergedCoverage.addStatement)
 
     Serializer.serialize(mergedCoverage, outputPath, ctx.settings.sourceroot.value)
 
+    result
+
   private def isClassIncluded(sym: Symbol)(using Context): Boolean =
     val fqn = sym.fullName.toText(ctx.printerFn(ctx)).show
     coverageExcludeClasslikePatterns.isEmpty || !coverageExcludeClasslikePatterns.exists(
@@ -275,9 +282,6 @@ class InstrumentCoverage extends MacroTransform with IdentityDenotTransformer:
         InstrumentedParts.singleExprTree(coverageCall, transformed)
 
     override def transform(tree: Tree)(using Context): Tree =
-      val path = tree.sourcePos.source.file.absolute.jpath
-      if path != null then lastCompiledFiles += path.toString
-
       inContext(transformCtx(tree)) { // necessary to position inlined code properly
         tree match
           // simple cases