diff --git a/dokka-runners/dokka-gradle-plugin/src/main/kotlin/DokkaBasePlugin.kt b/dokka-runners/dokka-gradle-plugin/src/main/kotlin/DokkaBasePlugin.kt
index 3b9a7ee79f..b308e4a2d2 100644
--- a/dokka-runners/dokka-gradle-plugin/src/main/kotlin/DokkaBasePlugin.kt
+++ b/dokka-runners/dokka-gradle-plugin/src/main/kotlin/DokkaBasePlugin.kt
@@ -208,6 +208,15 @@ constructor(
             sourceSetScope.convention(sourceSetScopeConvention)
 
             suppressGeneratedFiles.convention(true)
+            suppressedFiles.from(
+                suppressGeneratedFiles.map { suppressGenerated ->
+                    if (suppressGenerated) {
+                        layout.buildDirectory.dir("generated")
+                    } else {
+                        objects.fileCollection()
+                    }
+                }
+            )
 
             sourceLinks.configureEach {
                 localDirectory.convention(layout.projectDirectory)
diff --git a/dokka-runners/dokka-gradle-plugin/src/main/kotlin/engine/parameters/DokkaSourceSetSpec.kt b/dokka-runners/dokka-gradle-plugin/src/main/kotlin/engine/parameters/DokkaSourceSetSpec.kt
index 4277192b2d..9eeb654051 100644
--- a/dokka-runners/dokka-gradle-plugin/src/main/kotlin/engine/parameters/DokkaSourceSetSpec.kt
+++ b/dokka-runners/dokka-gradle-plugin/src/main/kotlin/engine/parameters/DokkaSourceSetSpec.kt
@@ -5,6 +5,7 @@ package org.jetbrains.dokka.gradle.engine.parameters
 
 import org.gradle.api.*
 import org.gradle.api.file.ConfigurableFileCollection
+import org.gradle.api.file.FileCollection
 import org.gradle.api.model.ObjectFactory
 import org.gradle.api.plugins.ExtensionAware
 import org.gradle.api.provider.Property
@@ -177,8 +178,7 @@ constructor(
      *
      * By default, source roots are deduced from information provided by the Kotlin Gradle plugin.
      */
-    @get:InputFiles
-    @get:PathSensitive(PathSensitivity.RELATIVE)
+    @get:Internal // tracked by `inputSourceFiles`
     abstract val sourceRoots: ConfigurableFileCollection
 
     /**
@@ -263,12 +263,12 @@ constructor(
      * Directories or individual files that should be suppressed, meaning declarations from them
      * will be not documented.
      *
-     * Will be concatenated with generated files if [suppressGeneratedFiles] is set to `false`.
+     * Will be concatenated with generated files if [suppressGeneratedFiles] is set to `true`.
      */
-    @get:InputFiles
-    @get:PathSensitive(PathSensitivity.RELATIVE)
+    @get:Internal // tracked by `inputSourceFiles`
     abstract val suppressedFiles: ConfigurableFileCollection
 
+
     /**
      * Whether to document/analyze generated files.
      *
@@ -444,6 +444,18 @@ constructor(
     abstract val noJdkLink: Property<Boolean>
     //endregion
 
+    // this is just for task input tracking, it's not used anywhere
+    @Suppress("unused")
+    @get:InputFiles
+    @get:IgnoreEmptyDirectories
+    @get:PathSensitive(PathSensitivity.RELATIVE)
+    internal val inputSourceFiles: FileCollection
+        get() = sourceRoots.asFileTree.filter { sourceFile ->
+            suppressedFiles.none { suppressedFile ->
+                sourceFile.startsWith(suppressedFile)
+            }
+        }
+
     companion object {
 
         /**
diff --git a/dokka-runners/dokka-gradle-plugin/src/test/kotlin/engine/parameters/DokkaSourceSetSpecTest.kt b/dokka-runners/dokka-gradle-plugin/src/test/kotlin/engine/parameters/DokkaSourceSetSpecTest.kt
index c7d9bc62ae..0fe7c11ea6 100644
--- a/dokka-runners/dokka-gradle-plugin/src/test/kotlin/engine/parameters/DokkaSourceSetSpecTest.kt
+++ b/dokka-runners/dokka-gradle-plugin/src/test/kotlin/engine/parameters/DokkaSourceSetSpecTest.kt
@@ -107,7 +107,7 @@ class DokkaSourceSetSpecTest : FunSpec({
             dss.suppressGeneratedFiles.orNull shouldBe true
         }
         test("suppressedFiles") {
-            dss.suppressedFiles.shouldBeEmpty()
+            dss.suppressedFiles.toList() shouldBe listOf(project.file("build/generated"))
         }
     }
 
diff --git a/dokka-runners/dokka-gradle-plugin/src/testFunctional/kotlin/SuppressGeneratedFilesFunctionalTest.kt b/dokka-runners/dokka-gradle-plugin/src/testFunctional/kotlin/SuppressGeneratedFilesFunctionalTest.kt
new file mode 100644
index 0000000000..2a29c6d305
--- /dev/null
+++ b/dokka-runners/dokka-gradle-plugin/src/testFunctional/kotlin/SuppressGeneratedFilesFunctionalTest.kt
@@ -0,0 +1,131 @@
+/*
+ * Copyright 2014-2024 JetBrains s.r.o. Use of this source code is governed by the Apache 2.0 license.
+ */
+package org.jetbrains.dokka.gradle
+
+import io.kotest.core.spec.style.FunSpec
+import io.kotest.matchers.paths.shouldExist
+import io.kotest.matchers.string.shouldContain
+import io.kotest.matchers.string.shouldNotContain
+import org.jetbrains.dokka.gradle.internal.DokkaConstants.DOKKA_VERSION
+import org.jetbrains.dokka.gradle.utils.*
+import java.nio.file.Path
+import kotlin.io.path.readText
+
+class SuppressGeneratedFilesFunctionalTest : FunSpec({
+
+    context("suppressGeneratedFiles") {
+
+        test("when suppressGeneratedFiles is true, generated files should be suppressed") {
+            val project = createProject(suppressGeneratedFiles = true)
+
+            project.runner
+                .addArguments(
+                    ":dokkaGeneratePublicationHtml",
+                    "--rerun-tasks",
+                    "--stacktrace",
+                )
+                .build {
+                    val htmlContent = project.projectDir
+                        .resolve("build/dokka/html/suppress-generated-files-true/[root]/index.html")
+                        .also(Path::shouldExist)
+                        .readText()
+                    htmlContent shouldContain "MyClass"
+                    htmlContent shouldNotContain "GeneratedClass"
+                    htmlContent shouldNotContain "GeneratedJavaClass"
+                }
+        }
+
+        test("when suppressGeneratedFiles is false, generated files should be documented") {
+            val project = createProject(suppressGeneratedFiles = false)
+
+            project.runner
+                .addArguments(
+                    ":dokkaGeneratePublicationHtml",
+                    "--rerun-tasks",
+                    "--stacktrace",
+                )
+                .build {
+                    val htmlContent = project.projectDir
+                        .resolve("build/dokka/html/suppress-generated-files-false/[root]/index.html")
+                        .also(Path::shouldExist)
+                        .readText()
+                    htmlContent shouldContain "MyClass"
+                    htmlContent shouldContain "GeneratedClass"
+                    htmlContent shouldContain "GeneratedJavaClass"
+                }
+        }
+    }
+})
+
+private fun createProject(
+    suppressGeneratedFiles: Boolean
+): GradleProjectTest = gradleKtsProjectTest("suppress-generated-files-$suppressGeneratedFiles") {
+    buildGradleKts = """
+        |plugins {
+        |    kotlin("jvm") version embeddedKotlinVersion
+        |    id("org.jetbrains.dokka") version "$DOKKA_VERSION"
+        |}
+        |
+        |dokka {
+        |    dokkaSourceSets.configureEach {
+        |        suppressGeneratedFiles.set(${suppressGeneratedFiles})
+        |        // emulate generated sources added, for example by KSP
+        |        sourceRoots.from("build/generated")
+        |    }
+        |}
+        |""".trimMargin()
+
+    dir("src/main/kotlin") {
+        createKotlinFile(
+            "MyClass.kt",
+            """
+            |/**
+            | * A regular class that should be documented
+            | */
+            |class MyClass {
+            |    /**
+            |     * A function that should be documented
+            |     */
+            |    fun regularFunction() = "Hello"
+            |}
+            |""".trimMargin()
+        )
+    }
+
+    dir("build/generated/ksp/main") {
+        createKotlinFile(
+            "GeneratedClass.kt",
+            """
+            |/**
+            | * A generated class that should NOT be documented
+            | */
+            |class GeneratedClass {
+            |    /**
+            |     * A generated function that should NOT be documented
+            |     */
+            |    fun generatedFunction() = "Generated"
+            |}
+            |""".trimMargin()
+        )
+    }
+
+    dir("build/generated/apt/java/main") {
+        createFile(
+            "GeneratedJavaClass.java",
+            """
+            |/**
+            | * A generated Java class that should NOT be documented
+            | */
+            |public class GeneratedJavaClass {
+            |    /**
+            |     * A generated method that should NOT be documented
+            |     */
+            |    public String generatedMethod() {
+            |        return "Generated Java";
+            |    }
+            |}
+            |""".trimMargin()
+        )
+    }
+}