diff --git a/plugins/kapt3/kapt3-base/src/org/jetbrains/kotlin/kapt3/base/incremental/incrementalProcessors.kt b/plugins/kapt3/kapt3-base/src/org/jetbrains/kotlin/kapt3/base/incremental/incrementalProcessors.kt
index 958ee45bb29..57fcddca9d6 100644
--- a/plugins/kapt3/kapt3-base/src/org/jetbrains/kotlin/kapt3/base/incremental/incrementalProcessors.kt
+++ b/plugins/kapt3/kapt3-base/src/org/jetbrains/kotlin/kapt3/base/incremental/incrementalProcessors.kt
@@ -124,15 +124,15 @@ internal class AnnotationProcessorDependencyCollector(private val runtimeProcTyp
     }
 }
 
-private fun getSrcFiles(elements: Array<out Element?>): List<File> {
+private fun getSrcFiles(elements: Array<out Element?>): Set<File> {
     return elements.filterNotNull().mapNotNull { elem ->
         var origin = elem
         while (origin.enclosingElement != null && origin.enclosingElement !is PackageElement) {
             origin = origin.enclosingElement
         }
         val uri = (origin as? Symbol.ClassSymbol)?.sourcefile?.toUri()?.takeIf { it.isAbsolute }
-        uri?.let { File(it) }
-    }
+        uri?.let { File(it).canonicalFile }
+    }.toSet()
 }
 
 enum class DeclaredProcType {
diff --git a/plugins/kapt3/kapt3-base/test/org/jetbrains/kotlin/kapt3/base/incremental/IsolatingIncrementalProcessorTest.kt b/plugins/kapt3/kapt3-base/test/org/jetbrains/kotlin/kapt3/base/incremental/IsolatingIncrementalProcessorTest.kt
index 412c5733cf1..223fa12b06a 100644
--- a/plugins/kapt3/kapt3-base/test/org/jetbrains/kotlin/kapt3/base/incremental/IsolatingIncrementalProcessorTest.kt
+++ b/plugins/kapt3/kapt3-base/test/org/jetbrains/kotlin/kapt3/base/incremental/IsolatingIncrementalProcessorTest.kt
@@ -107,4 +107,17 @@ class IsolationgIncrementalProcessorTest {
             ), isolating[1].getGeneratedToSources()
         )
     }
+
+    @Test
+    fun testIsolatingWithMultipleOriginatingElements() {
+        val srcFiles = listOf("User.java", "Observable.java").map { File(TEST_DATA_DIR, it) }
+        val isolating = listOf(ReportTwoOriginElements().toIsolating())
+        runAnnotationProcessing(srcFiles, isolating, generatedSources)
+
+        assertEquals(
+            mapOf(
+                generatedSources.resolve("test/UserGenerated.java") to File("plugins/kapt3/kapt3-base/testData/runner/incremental/User.java").absoluteFile
+            ), isolating[0].getGeneratedToSources()
+        )
+    }
 }
diff --git a/plugins/kapt3/kapt3-base/test/org/jetbrains/kotlin/kapt3/base/incremental/fixtures.kt b/plugins/kapt3/kapt3-base/test/org/jetbrains/kotlin/kapt3/base/incremental/fixtures.kt
index c0eb785cea6..100e791fe70 100644
--- a/plugins/kapt3/kapt3-base/test/org/jetbrains/kotlin/kapt3/base/incremental/fixtures.kt
+++ b/plugins/kapt3/kapt3-base/test/org/jetbrains/kotlin/kapt3/base/incremental/fixtures.kt
@@ -145,6 +145,20 @@ class SimpleGeneratingIfTypeDoesNotExist: SimpleProcessor() {
             }
         }
 
+        return false
+    }
+}
+
+open class ReportTwoOriginElements : SimpleProcessor() {
+    override fun process(annotations: MutableSet<out TypeElement>, roundEnv: RoundEnvironment): Boolean {
+        if (annotations.isEmpty()) return false
+
+        roundEnv.getElementsAnnotatedWith(annotations.single()).forEach {
+            it as TypeElement
+            // Report 2 elements from the same file as originating
+            filer.createSourceFile("${it.qualifiedName}Generated", it, it).openWriter().use { it.write("") }
+        }
+
         return false
     }
 }
\ No newline at end of file