diff --git a/backend.native/compiler/ir/backend.native/src/org/jetbrains/kotlin/backend/konan/llvm/coverage/CoverageManager.kt b/backend.native/compiler/ir/backend.native/src/org/jetbrains/kotlin/backend/konan/llvm/coverage/CoverageManager.kt
index 7cd2ed532c8..916e0920b50 100644
--- a/backend.native/compiler/ir/backend.native/src/org/jetbrains/kotlin/backend/konan/llvm/coverage/CoverageManager.kt
+++ b/backend.native/compiler/ir/backend.native/src/org/jetbrains/kotlin/backend/konan/llvm/coverage/CoverageManager.kt
@@ -65,7 +65,8 @@ internal class CoverageManager(val context: Context) {
         val coveredUserCode = if (shouldCoverProgram) setOf(context.moduleDescriptor) else emptySet()
         val coveredLibs = context.irModules.filter { it.key in librariesToCover }.values
                 .map { it.descriptor }.toSet()
-        coveredLibs + coveredUserCode
+        val coveredIncludedLibs = if (shouldCoverProgram) context.getIncludedLibraryDescriptors().toSet() else emptySet()
+        coveredLibs + coveredUserCode + coveredIncludedLibs
     }
 
     private fun fileCoverageFilter(file: IrFile) =
diff --git a/backend.native/tests/build.gradle b/backend.native/tests/build.gradle
index 2554701da03..b838778f66e 100644
--- a/backend.native/tests/build.gradle
+++ b/backend.native/tests/build.gradle
@@ -3703,16 +3703,7 @@ standaloneTest("coverage_basic_program") {
     flags = ["-Xcoverage-file=$coverageFile", "-Xcoverage", "-entry", "coverage.basic.program.main"]
     source = "$projectDir/coverage/basic/program/main.kt"
 
-    doFirst { file(coverageFile).delete() }
-
     doLast {
-        if (twoStageEnabled) {
-            // If two-stage compilation is enabled, no sources are passed to the compiler when a final binary is generated.
-            // So according to -Xcoverage flag semantics it must provide no coverage info.
-            assert !file(coverageFile).exists()
-            return
-        }
-
         execLlvm("llvm-profdata") {
             args "merge"
             args "$dir/program.profraw"