diff --git a/.github/workflows/check-api.yml b/.github/workflows/check-api.yml
index 444e56ed8d..a981a0f7eb 100644
--- a/.github/workflows/check-api.yml
+++ b/.github/workflows/check-api.yml
@@ -14,9 +14,10 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-java@v4
         with:
-          distribution: 'zulu'
-          java-version: 17
+          distribution: "temurin"
+          java-version: 21
       - uses: gradle/actions/setup-gradle@v4
         with:
+          cache-cleanup: always
           develocity-access-key: ${{ secrets.DEVELOCITY_ACCESS_KEY }}
       - run: ./gradlew apiCheck --stacktrace
diff --git a/.github/workflows/examples-build.yml b/.github/workflows/examples-build.yml
index 4648a61a75..ebb7b5adaf 100644
--- a/.github/workflows/examples-build.yml
+++ b/.github/workflows/examples-build.yml
@@ -33,10 +33,11 @@ jobs:
               - '${{ matrix.projects }}/**'
       - uses: actions/setup-java@v4
         with:
-          distribution: 'zulu'
-          java-version: 17
+          distribution: "temurin"
+          java-version: 21
       - uses: gradle/actions/setup-gradle@v4
         with:
+          cache-cleanup: always
           develocity-access-key: ${{ secrets.DEVELOCITY_ACCESS_KEY }}
       - run: ./gradlew build --no-daemon --stacktrace
         working-directory: ${{ matrix.projects }}
@@ -63,10 +64,11 @@ jobs:
               - '${{ matrix.projects }}/**'
       - uses: actions/setup-java@v4
         with:
-          distribution: 'zulu'
-          java-version: 17
+          distribution: "temurin"
+          java-version: 21
       - uses: gradle/actions/setup-gradle@v4
         with:
+          cache-cleanup: always
           develocity-access-key: ${{ secrets.DEVELOCITY_ACCESS_KEY }}
       - run: ./gradlew dokkaHtml --no-daemon --stacktrace
         working-directory: ${{ matrix.projects }}
@@ -87,10 +89,11 @@ jobs:
               - 'examples/gradle/dokka-library-publishing-example/**'
       - uses: actions/setup-java@v4
         with:
-          distribution: 'zulu'
-          java-version: 17
+          distribution: "temurin"
+          java-version: 21
       - uses: gradle/actions/setup-gradle@v4
         with:
+          cache-cleanup: always
           develocity-access-key: ${{ secrets.DEVELOCITY_ACCESS_KEY }}
       - run: ./gradlew ${{ matrix.tasks }} --no-daemon --stacktrace
         working-directory: examples/gradle/dokka-library-publishing-example
@@ -113,10 +116,11 @@ jobs:
               - '${{ matrix.dir }}/**'
       - uses: actions/setup-java@v4
         with:
-          distribution: 'zulu'
-          java-version: 17
+          distribution: "temurin"
+          java-version: 21
       - uses: gradle/actions/setup-gradle@v4
         with:
+          cache-cleanup: always
           develocity-access-key: ${{ secrets.DEVELOCITY_ACCESS_KEY }}
       - run: ./gradlew ${{ matrix.task }} --no-daemon --stacktrace
         working-directory: ${{ matrix.dir }}
@@ -135,9 +139,8 @@ jobs:
           working-directory: examples/maven
       - uses: actions/setup-java@v4
         with:
-          distribution: 'zulu'
-          java-version: 17
-          cache: 'maven'
+          distribution: "temurin"
+          java-version: 21
       - run: mvn compile dokka:dokka
         working-directory: examples/maven
         if: steps.filter.outputs.examples_changed == 'true'
diff --git a/.github/workflows/gh-pages-deploy-dev-docs.yml b/.github/workflows/gh-pages-deploy-dev-docs.yml
index e1474e5f62..39962d5f9e 100644
--- a/.github/workflows/gh-pages-deploy-dev-docs.yml
+++ b/.github/workflows/gh-pages-deploy-dev-docs.yml
@@ -20,10 +20,11 @@ jobs:
           path: dokka
       - uses: actions/setup-java@v4
         with:
-          distribution: 'zulu'
-          java-version: 17
+          distribution: "temurin"
+          java-version: 21
       - uses: gradle/actions/setup-gradle@v4
         with:
+          cache-cleanup: always
           develocity-access-key: ${{ secrets.DEVELOCITY_ACCESS_KEY }}
       - name: Get current Dokka version
         run: echo "DOKKA_VERSION=`./gradlew :properties | grep '^version:.*' | cut -d ' ' -f 2`" >> $GITHUB_ENV
diff --git a/.github/workflows/gh-pages-deploy-examples.yml b/.github/workflows/gh-pages-deploy-examples.yml
index 1e2a1a5556..4abe3cd815 100644
--- a/.github/workflows/gh-pages-deploy-examples.yml
+++ b/.github/workflows/gh-pages-deploy-examples.yml
@@ -30,10 +30,11 @@ jobs:
               - 'examples/gradle/${{ matrix.projects }}/**'
       - uses: actions/setup-java@v4
         with:
-          distribution: 'zulu'
-          java-version: 17
+          distribution: "temurin"
+          java-version: 21
       - uses: gradle/actions/setup-gradle@v4
         with:
+          cache-cleanup: always
           develocity-access-key: ${{ secrets.DEVELOCITY_ACCESS_KEY }}
       - name: Build html
         run: ./gradlew dokkaHtml --no-daemon --stacktrace
@@ -65,11 +66,11 @@ jobs:
               - 'examples/gradle/${{ matrix.projects }}/**'
       - uses: actions/setup-java@v4
         with:
-          distribution: 'zulu'
-          java-version: 17
-          cache: 'maven'
+          distribution: "temurin"
+          java-version: 21
       - uses: gradle/actions/setup-gradle@v4
         with:
+          cache-cleanup: always
           develocity-access-key: ${{ secrets.DEVELOCITY_ACCESS_KEY }}
       - name: Build html
         run: ./gradlew dokkaHtmlMultiModule --no-daemon --stacktrace
diff --git a/.github/workflows/preview-publish-ga.yml b/.github/workflows/preview-publish-ga.yml
index 0ea176f310..554186eb1f 100644
--- a/.github/workflows/preview-publish-ga.yml
+++ b/.github/workflows/preview-publish-ga.yml
@@ -18,10 +18,11 @@ jobs:
         uses: actions/checkout@v4
       - uses: actions/setup-java@v4
         with:
-          distribution: 'zulu'
-          java-version: 17
+          distribution: "temurin"
+          java-version: 21
       - uses: gradle/actions/setup-gradle@v4
         with:
+          cache-cleanup: always
           develocity-access-key: ${{ secrets.DEVELOCITY_ACCESS_KEY }}
       - name: Document coroutines
         run: ./gradlew :dokka-integration-tests:gradle:testExternalProjectKotlinxCoroutines --stacktrace "-Dorg.gradle.jvmargs=-Xmx2g -XX:MaxMetaspaceSize=500m"
@@ -44,10 +45,11 @@ jobs:
         uses: actions/checkout@v4
       - uses: actions/setup-java@v4
         with:
-          distribution: 'zulu'
-          java-version: 17
+          distribution: "temurin"
+          java-version: 21
       - uses: gradle/actions/setup-gradle@v4
         with:
+          cache-cleanup: always
           develocity-access-key: ${{ secrets.DEVELOCITY_ACCESS_KEY }}
       - name: Document serialization
         run: ./gradlew :dokka-integration-tests:gradle:testExternalProjectKotlinxSerialization --stacktrace "-Dorg.gradle.jvmargs=-Xmx2g -XX:MaxMetaspaceSize=500m"
@@ -70,10 +72,11 @@ jobs:
         uses: actions/checkout@v4
       - uses: actions/setup-java@v4
         with:
-          distribution: 'zulu'
-          java-version: 17
+          distribution: "temurin"
+          java-version: 21
       - uses: gradle/actions/setup-gradle@v4
         with:
+          cache-cleanup: always
           develocity-access-key: ${{ secrets.DEVELOCITY_ACCESS_KEY }}
       - name: Document biojava-core
         run: ./gradlew :dokka-integration-tests:maven:testExternalProjectBioJava --stacktrace
diff --git a/.github/workflows/preview-publish-web-s3.yml b/.github/workflows/preview-publish-web-s3.yml
index c0aedf6a7f..e06bcc86a4 100644
--- a/.github/workflows/preview-publish-web-s3.yml
+++ b/.github/workflows/preview-publish-web-s3.yml
@@ -15,10 +15,11 @@ jobs:
         uses: actions/checkout@v4
       - uses: actions/setup-java@v4
         with:
-          distribution: 'zulu'
-          java-version: 17
+          distribution: "temurin"
+          java-version: 21
       - uses: gradle/actions/setup-gradle@v4
         with:
+          cache-cleanup: always
           develocity-access-key: ${{ secrets.DEVELOCITY_ACCESS_KEY }}
       - name: Document coroutines
         run: ./gradlew :dokka-integration-tests:gradle:testExternalProjectKotlinxCoroutines --stacktrace "-Dorg.gradle.jvmargs=-Xmx2g -XX:MaxMetaspaceSize=500m"
@@ -43,10 +44,11 @@ jobs:
         uses: actions/checkout@v4
       - uses: actions/setup-java@v4
         with:
-          distribution: 'zulu'
-          java-version: 17
+          distribution: "temurin"
+          java-version: 21
       - uses: gradle/actions/setup-gradle@v4
         with:
+          cache-cleanup: always
           develocity-access-key: ${{ secrets.DEVELOCITY_ACCESS_KEY }}
       - name: Document serialization
         run: ./gradlew :dokka-integration-tests:gradle:testExternalProjectKotlinxSerialization --stacktrace "-Dorg.gradle.jvmargs=-Xmx2g -XX:MaxMetaspaceSize=500m"
@@ -71,10 +73,11 @@ jobs:
         uses: actions/checkout@v4
       - uses: actions/setup-java@v4
         with:
-          distribution: 'zulu'
-          java-version: 17
+          distribution: "temurin"
+          java-version: 21
       - uses: gradle/actions/setup-gradle@v4
         with:
+          cache-cleanup: always
           develocity-access-key: ${{ secrets.DEVELOCITY_ACCESS_KEY }}
       - name: Generate ui-showcase documentation
         run: ./gradlew :dokka-integration-tests:gradle:testUiShowcaseProject
@@ -99,11 +102,11 @@ jobs:
         uses: actions/checkout@v4
       - uses: actions/setup-java@v4
         with:
-          distribution: 'zulu'
-          java-version: 17
-          cache: 'maven'
+          distribution: "temurin"
+          java-version: 21
       - uses: gradle/actions/setup-gradle@v4
         with:
+          cache-cleanup: always
           develocity-access-key: ${{ secrets.DEVELOCITY_ACCESS_KEY }}
       - name: Document biojava-core
         run: ./gradlew :dokka-integration-tests:maven:testExternalProjectBioJava --stacktrace
diff --git a/.github/workflows/tests-smoke.yml b/.github/workflows/tests-smoke.yml
index 9e1279fa5f..d74dbb1b13 100644
--- a/.github/workflows/tests-smoke.yml
+++ b/.github/workflows/tests-smoke.yml
@@ -25,10 +25,11 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-java@v4
         with:
-          distribution: 'zulu'
-          java-version: 17
+          distribution: "temurin"
+          java-version: 21
       - uses: gradle/actions/setup-gradle@v4
         with:
+          cache-cleanup: always
           develocity-access-key: ${{ secrets.DEVELOCITY_ACCESS_KEY }}
       - name: Run tests
         run: >
diff --git a/.github/workflows/tests-thorough.yml b/.github/workflows/tests-thorough.yml
index c5586f73d6..0a66f594ce 100644
--- a/.github/workflows/tests-thorough.yml
+++ b/.github/workflows/tests-thorough.yml
@@ -23,10 +23,11 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-java@v4
         with:
-          distribution: 'zulu'
-          java-version: 17
+          distribution: "temurin"
+          java-version: 21
       - uses: gradle/actions/setup-gradle@v4
         with:
+          cache-cleanup: always
           develocity-access-key: ${{ secrets.DEVELOCITY_ACCESS_KEY }}
       - name: Run tests
         run: >
diff --git a/.gitignore b/.gitignore
index f252364f0e..262a92b2a5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -29,6 +29,9 @@ hs_err_pid*
 .gradle
 build/
 
+# FIXME Remove when Gradle Daemon JVM can be auto-provisioned. See build-logic/src/main/kotlin/dokkabuild/utils/GradleDaemonJvm.kt
+gradle/gradle-daemon-jvm.properties
+
 # Avoid ignoring Gradle wrapper jar file (.jar files are usually ignored)
 !gradle-wrapper.jar
 
diff --git a/build-logic/build.gradle.kts b/build-logic/build.gradle.kts
index 619e61d74b..fdfcd0a25e 100644
--- a/build-logic/build.gradle.kts
+++ b/build-logic/build.gradle.kts
@@ -3,13 +3,19 @@
  */
 
 import org.gradle.kotlin.dsl.support.expectedKotlinDslPluginsVersion
+import org.jetbrains.kotlin.gradle.dsl.JvmTarget
+import org.jetbrains.kotlin.gradle.dsl.KotlinJvmCompilerOptions
+import org.jetbrains.kotlin.gradle.tasks.KotlinJvmCompile
+import kotlin.jvm.optionals.getOrElse
 
 plugins {
     `kotlin-dsl`
 }
 
 kotlin {
-    jvmToolchain(11)
+    jvmToolchain {
+        languageVersion = libs.versions.gradleDaemonJvm.map(String::toInt).map(JavaLanguageVersion::of)
+    }
 }
 
 dependencies {
diff --git a/build-logic/src/main/kotlin/dokkabuild/utils/GradleDaemonJvm.kt b/build-logic/src/main/kotlin/dokkabuild/utils/GradleDaemonJvm.kt
new file mode 100644
index 0000000000..bac647aa77
--- /dev/null
+++ b/build-logic/src/main/kotlin/dokkabuild/utils/GradleDaemonJvm.kt
@@ -0,0 +1,88 @@
+/*
+ * Copyright 2014-2024 JetBrains s.r.o. Use of this source code is governed by the Apache 2.0 license.
+ */
+
+package dokkabuild.utils
+
+import org.gradle.api.JavaVersion
+import org.gradle.api.Project
+import org.gradle.api.logging.Logging
+import org.gradle.api.provider.Provider
+import org.gradle.api.tasks.TaskProvider
+import org.gradle.buildconfiguration.tasks.UpdateDaemonJvm
+import org.gradle.jvm.toolchain.JavaLanguageVersion
+import org.gradle.jvm.toolchain.JavaToolchainService
+import org.gradle.kotlin.dsl.assign
+import org.gradle.kotlin.dsl.invoke
+import org.gradle.kotlin.dsl.support.serviceOf
+
+/**
+ * Lazily configure the version of Java Gradle uses to run the daemon.
+ *
+ * To maximise Build Cache hits the same JDK version should be used to run Gradle on all machines.
+ *
+ * Gradle has an incubating feature to set the Daemon JVM
+ * https://docs.gradle.org/current/userguide/gradle_daemon.html#sec:daemon_jvm_criteria,
+ * but it doesn't auto-download the required JVM. This is annoying, because Gradle will just fail
+ * until the user manually installs the required JVM.
+ *
+ * Instead, this function configures Gradle so it will only set the Daemon JVM if the
+ * required JDK is installed.
+ *
+ * This custom logic can be removed when Gradle supports auto-provisioning of the Daemon JVM
+ * https://github.com/gradle/gradle/pull/29166
+ */
+@Suppress("UnstableApiUsage")
+fun configureGradleDaemonJvm(
+    project: Project,
+    updateDaemonJvm: TaskProvider<UpdateDaemonJvm>,
+    gradleDaemonJvmVersion: Provider<JavaVersion>,
+) {
+    require(project.rootProject == project) {
+        "Gradle Daemon must be configured in the root project, but was configured in ${project.displayName}."
+    }
+
+    @Suppress("UnstableApiUsage")
+    updateDaemonJvm {
+        jvmVersion = gradleDaemonJvmVersion.map(JavaVersion::toVersion)
+
+        val javaToolchains = project.serviceOf<JavaToolchainService>()
+        val isGradleDaemonJvmVersionInstalled = gradleDaemonJvmVersion.isInstalled(javaToolchains)
+        inputs.property("isGradleDaemonJvmVersionInstalled", isGradleDaemonJvmVersionInstalled)
+        onlyIf("Valid JVM is installed") { isGradleDaemonJvmVersionInstalled.get() }
+    }
+
+    // Depend on some common tasks, so the Daemon JVM properties file will be generated automatically.
+    project.defaultTasks(updateDaemonJvm.name)
+    project.tasks
+        .matching { it.name in setOf("prepareKotlinIdeaImport", "prepareKotlinBuildScriptModel", "assemble") }
+        .configureEach {
+            dependsOn(updateDaemonJvm)
+        }
+}
+
+/**
+ * Determine if the [JavaToolchainService] can detect, or automatically install,
+ * a toolchain for this [JavaVersion].
+ */
+private fun Provider<JavaVersion>.isInstalled(
+    javaToolchains: JavaToolchainService
+): Provider<Boolean> {
+    // Must catch exceptions because Toolchains don't properly support the Provider API.
+    // See https://github.com/gradle/gradle/issues/29758
+    return map { version ->
+        val launcher = try {
+            javaToolchains
+                .launcherFor { languageVersion = JavaLanguageVersion.of(version.majorVersion) }
+                .orNull
+        } catch (ex: Exception) {
+            null
+        }
+        if (launcher == null) {
+            logger.lifecycle("i: Could not find JDK $version to run Gradle Daemon. Build performance may be impacted.")
+        }
+        launcher == null
+    }
+}
+
+private val logger = Logging.getLogger("dokkabuild.GradleDaemonJvm")
diff --git a/build-settings-logic/build.gradle.kts b/build-settings-logic/build.gradle.kts
index 78114e59b1..c682db1792 100644
--- a/build-settings-logic/build.gradle.kts
+++ b/build-settings-logic/build.gradle.kts
@@ -9,7 +9,9 @@ plugins {
 description = "Conventions for use in settings.gradle.kts scripts"
 
 kotlin {
-    jvmToolchain(11)
+    jvmToolchain {
+        languageVersion = libs.versions.gradleDaemonJvm.map(String::toInt).map(JavaLanguageVersion::of)
+    }
 }
 
 dependencies {
diff --git a/build.gradle.kts b/build.gradle.kts
index e4c294a282..c67bbfd6dd 100644
--- a/build.gradle.kts
+++ b/build.gradle.kts
@@ -1,6 +1,7 @@
 /*
  * Copyright 2014-2024 JetBrains s.r.o. Use of this source code is governed by the Apache 2.0 license.
  */
+import dokkabuild.utils.configureGradleDaemonJvm
 
 plugins {
     id("dokkabuild.base")
@@ -123,3 +124,9 @@ idea {
         )
     }
 }
+
+configureGradleDaemonJvm(
+    project = project,
+    updateDaemonJvm = tasks.updateDaemonJvm,
+    gradleDaemonJvmVersion = libs.versions.gradleDaemonJvm.map(JavaVersion::toVersion),
+)
diff --git a/gradle/daemon-jvm.properties b/gradle/daemon-jvm.properties
new file mode 100644
index 0000000000..63e5bbdf48
--- /dev/null
+++ b/gradle/daemon-jvm.properties
@@ -0,0 +1,2 @@
+#This file is generated by updateDaemonJvm
+toolchainVersion=21
diff --git a/gradle/libs.versions.toml b/gradle/libs.versions.toml
index b5608a6b88..22382844b4 100644
--- a/gradle/libs.versions.toml
+++ b/gradle/libs.versions.toml
@@ -63,6 +63,9 @@ junit = "5.9.3"
 kotest = "5.6.2"
 eclipse-jgit = "5.13.3.202401111512-r" # jgit 6.X requires Java 11 to run
 
+# JDK used to run Gradle Daemon. (Should be the same as jvmCompiler, but could be higher or lower.)
+gradleDaemonJvm = "21"
+
 [libraries]
 
 #### Kotlin Libs ####
diff --git a/gradle/wrapper/gradle-wrapper.jar b/gradle/wrapper/gradle-wrapper.jar
index e6441136f3..2c3521197d 100644
Binary files a/gradle/wrapper/gradle-wrapper.jar and b/gradle/wrapper/gradle-wrapper.jar differ