diff --git a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KlibBasedMppIT.kt b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KlibBasedMppIT.kt
index d31233a5f1e..e041aea3f0d 100644
--- a/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KlibBasedMppIT.kt
+++ b/libraries/tools/kotlin-gradle-plugin-integration-tests/src/test/kotlin/org/jetbrains/kotlin/gradle/KlibBasedMppIT.kt
@@ -30,11 +30,26 @@ class KlibBasedMppIT : BaseGradleIT() {
         """.trimIndent())
     }
 
+    @Test
+    fun testPublishingAndConsumptionWithEmptySourceSet() = testBuildWithDependency {
+        // KT-36674
+        projectDir.resolve("$dependencyModuleName/src/$hostSpecificSourceSet").run {
+            assertTrue { isDirectory }
+            deleteRecursively()
+        }
+        publishProjectDepAndAddDependency(validateHostSpecificPublication = false)
+    }
+
     @Test
     fun testBuildWithPublishedDependency() = testBuildWithDependency {
+        publishProjectDepAndAddDependency(validateHostSpecificPublication = true)
+    }
+
+    private fun Project.publishProjectDepAndAddDependency(validateHostSpecificPublication: Boolean) {
         build(":$dependencyModuleName:publish") {
             assertSuccessful()
-            checkPublishedHostSpecificMetadata(this@build)
+            if (validateHostSpecificPublication)
+                checkPublishedHostSpecificMetadata(this@build)
         }
 
         gradleBuildScript().appendText("\n" + """
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/GranularMetadataTransformation.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/GranularMetadataTransformation.kt
index 63d9221bfce..dddbe39e467 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/GranularMetadataTransformation.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/plugin/mpp/GranularMetadataTransformation.kt
@@ -371,30 +371,32 @@ private class JarArtifactMppDependencyMetadataExtractor(
 
         artifactBySourceSet.forEach { (sourceSetName, artifact) ->
             ZipFile(artifact).use { zip ->
-                val entries = zip.entries().asSequence().filter { it.name.startsWith("$sourceSetName/") }
+                val entries = zip.entries().asSequence().filter { it.name.startsWith("$sourceSetName/") }.toList()
 
                 // TODO: once IJ supports non-JAR metadata dependencies, extract to a directory, not a JAR
                 // Also, if both IJ and the CLI compiler can read metadata from a path inside a JAR, then no operations will be needed
-                val extension =
-                    projectStructureMetadata.sourceSetBinaryLayout[sourceSetName]?.archiveExtension
+
+                if (entries.any()) {
+                    val extension = projectStructureMetadata.sourceSetBinaryLayout[sourceSetName]?.archiveExtension
                         ?: SourceSetMetadataLayout.METADATA.archiveExtension
-                val extractToJarFile = transformedModuleRoot.resolve("$moduleString-$sourceSetName.$extension")
 
-                resultFiles[sourceSetName] = project.files(extractToJarFile)
+                    val extractToJarFile = transformedModuleRoot.resolve("$moduleString-$sourceSetName.$extension")
+                    resultFiles[sourceSetName] = project.files(extractToJarFile)
 
-                if (doProcessFiles) {
-                    ZipOutputStream(extractToJarFile.outputStream()).use { resultZipOutput ->
-                        for (entry in entries) {
-                            if (entry.isDirectory)
-                                continue
+                    if (doProcessFiles) {
+                        ZipOutputStream(extractToJarFile.outputStream()).use { resultZipOutput ->
+                            for (entry in entries) {
+                                if (entry.isDirectory)
+                                    continue
 
-                            // Drop the source set name from the entry path
-                            val resultEntry = ZipEntry(entry.name.substringAfter("/"))
+                                // Drop the source set name from the entry path
+                                val resultEntry = ZipEntry(entry.name.substringAfter("/"))
 
-                            zip.getInputStream(entry).use { inputStream ->
-                                resultZipOutput.putNextEntry(resultEntry)
-                                inputStream.copyTo(resultZipOutput)
-                                resultZipOutput.closeEntry()
+                                zip.getInputStream(entry).use { inputStream ->
+                                    resultZipOutput.putNextEntry(resultEntry)
+                                    inputStream.copyTo(resultZipOutput)
+                                    resultZipOutput.closeEntry()
+                                }
                             }
                         }
                     }
diff --git a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/metadata/KotlinMetadataTargetConfigurator.kt b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/metadata/KotlinMetadataTargetConfigurator.kt
index b8d21acc6d8..5b43a10eb45 100644
--- a/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/metadata/KotlinMetadataTargetConfigurator.kt
+++ b/libraries/tools/kotlin-gradle-plugin/src/main/kotlin/org/jetbrains/kotlin/gradle/targets/metadata/KotlinMetadataTargetConfigurator.kt
@@ -532,9 +532,9 @@ internal fun getPublishedPlatformCompilations(project: Project): Map<KotlinUsage
 
 internal fun Project.filesWithUnpackedArchives(from: FileCollection, extensions: Set<String>): FileCollection =
     project.files(project.provider {
-        from.map {
-            if (it.extension in extensions)
-                project.zipTree(it)
-            else it
+        from.mapNotNull {
+            if (it.extension in extensions) {
+                if (it.exists()) project.zipTree(it) else null
+            } else it
         }
     }).builtBy(from)
\ No newline at end of file