diff --git a/dokka-integration-tests/cli/src/integrationTest/kotlin/org/jetbrains/dokka/it/cli/CliIntegrationTest.kt b/dokka-integration-tests/cli/src/integrationTest/kotlin/org/jetbrains/dokka/it/cli/CliIntegrationTest.kt
index 8bab690bb34..b5387b1da92 100644
--- a/dokka-integration-tests/cli/src/integrationTest/kotlin/org/jetbrains/dokka/it/cli/CliIntegrationTest.kt
+++ b/dokka-integration-tests/cli/src/integrationTest/kotlin/org/jetbrains/dokka/it/cli/CliIntegrationTest.kt
@@ -374,4 +374,42 @@ class CliIntegrationTest : AbstractCliIntegrationTest() {
 
         assertTrue(dokkaOutputDir.isDirectory, "Missing dokka output directory")
     }
+
+    @Test
+    fun `relative paths in configuraiton should work`() {
+        val resourcePath =
+            javaClass.getResource("/my-file.json")?.toURI() ?: throw IllegalStateException("No JSON found!")
+        val jsonPath = File(resourcePath)
+
+        val dokkaOutputDir = File(projectDir, "output-relative")
+        assertTrue(dokkaOutputDir.mkdirs())
+        jsonPath.writeText(
+            jsonBuilder(
+                outputPath = dokkaOutputDir.invariantSeparatorsPath,
+                pluginsClasspath = basePluginJarFile.absoluteFile.invariantSeparatorsPath,
+                projectPath = "src", // relative path
+            )
+        )
+
+        ProcessBuilder(
+            "java", "-jar", cliJarFile.absolutePath, jsonPath.absolutePath
+        ).directory(projectDir).redirectErrorStream(true).start().also { process ->
+            val result = process.awaitProcessResult()
+            assertEquals(0, result.exitCode, "Expected exitCode 0 (Success)")
+        }
+
+        assertTrue(dokkaOutputDir.isDirectory, "Missing dokka output directory")
+
+        val htmlFiles = dokkaOutputDir.allHtmlFiles().map { it.relativeTo(dokkaOutputDir).path }.toList()
+
+        // check that both Kotlin and Java sources are processed
+
+        // kotlin:
+        assertContains(htmlFiles, "-dokka -example/it.basic/index.html")
+        assertContains(htmlFiles, "-dokka -example/it.basic/-public-class/public-documented-function.html")
+
+        // java:
+        assertContains(htmlFiles, "-dokka -example/it.basic.java/index.html")
+        assertContains(htmlFiles, "-dokka -example/it.basic.java/-sample-java-class/public-documented-function.html")
+    }
 }
diff --git a/dokka-subprojects/analysis-kotlin-descriptors-compiler/src/main/kotlin/org/jetbrains/dokka/analysis/kotlin/descriptors/compiler/translator/DefaultDescriptorToDocumentableTranslator.kt b/dokka-subprojects/analysis-kotlin-descriptors-compiler/src/main/kotlin/org/jetbrains/dokka/analysis/kotlin/descriptors/compiler/translator/DefaultDescriptorToDocumentableTranslator.kt
index 4d5611891f9..73adc2714c7 100644
--- a/dokka-subprojects/analysis-kotlin-descriptors-compiler/src/main/kotlin/org/jetbrains/dokka/analysis/kotlin/descriptors/compiler/translator/DefaultDescriptorToDocumentableTranslator.kt
+++ b/dokka-subprojects/analysis-kotlin-descriptors-compiler/src/main/kotlin/org/jetbrains/dokka/analysis/kotlin/descriptors/compiler/translator/DefaultDescriptorToDocumentableTranslator.kt
@@ -159,9 +159,14 @@ private class DokkaDescriptorVisitor(
     private val syntheticDocProvider = SyntheticDescriptorDocumentationProvider(kDocFinder, sourceSet)
 
     private fun Collection<DeclarationDescriptor>.filterDescriptorsInSourceSet() = filter {
-        it.toSourceElement.containingFile.toString().let { path ->
-            path.isNotBlank() && sourceSet.sourceRoots.any { root ->
-                Paths.get(path).startsWith(root.toPath())
+        val pathString = it.toSourceElement.containingFile.toString()
+        when {
+            pathString.isBlank() -> false
+            else -> {
+                val absolutePath = Paths.get(pathString).toAbsolutePath()
+                sourceSet.sourceRoots.any { root ->
+                    absolutePath.startsWith(root.toPath().toAbsolutePath())
+                }
             }
         }
     }
diff --git a/dokka-subprojects/analysis-kotlin-symbols/src/main/kotlin/org/jetbrains/dokka/analysis/kotlin/symbols/translators/DefaultSymbolToDocumentableTranslator.kt b/dokka-subprojects/analysis-kotlin-symbols/src/main/kotlin/org/jetbrains/dokka/analysis/kotlin/symbols/translators/DefaultSymbolToDocumentableTranslator.kt
index 298d0182ca2..cbe5348f1bf 100644
--- a/dokka-subprojects/analysis-kotlin-symbols/src/main/kotlin/org/jetbrains/dokka/analysis/kotlin/symbols/translators/DefaultSymbolToDocumentableTranslator.kt
+++ b/dokka-subprojects/analysis-kotlin-symbols/src/main/kotlin/org/jetbrains/dokka/analysis/kotlin/symbols/translators/DefaultSymbolToDocumentableTranslator.kt
@@ -109,11 +109,16 @@ internal class DokkaSymbolVisitor(
         get() = (psi as? KtModifierListOwner)?.hasExpectModifier() == true
 
     private fun <T : KtSymbol> Collection<T>.filterSymbolsInSourceSet() = filter {
-        it.psi?.containingFile?.virtualFile?.path?.let { path ->
-            path.isNotBlank() && sourceSet.sourceRoots.any { root ->
-                Paths.get(path).startsWith(root.toPath())
+        val pathString = it.psi?.containingFile?.virtualFile?.path
+        when {
+            pathString.isNullOrBlank() -> false
+            else -> {
+                val absolutePath = Paths.get(pathString).toAbsolutePath()
+                sourceSet.sourceRoots.any { root ->
+                    absolutePath.startsWith(root.toPath().toAbsolutePath())
+                }
             }
-        } == true
+        }
     }
 
     fun visitModule(): DModule {