diff --git a/docs/manual-configuration.md b/docs/manual-configuration.md
index 24d1be02..111b5100 100644
--- a/docs/manual-configuration.md
+++ b/docs/manual-configuration.md
@@ -38,7 +38,10 @@ javac -classpath semanticdb-javac.jar MyApplication.java
 If you're using Gradle.
 
 ```groovy
-compileOnly group: 'com.sourcegraph', name: 'semanticdb-javac', version: '@STABLE_VERSION@'
+// Option 1: if you are not using annotation processors
+compileOnly 'com.sourcegraph:semanticdb-javac:@STABLE_VERSION@'
+// Option 2: if you are using annotation processors
+annotationProcessor 'com.sourcegraph:semanticdb-javac:@STABLE_VERSION@'
 ```
 
 If you're using Maven.
diff --git a/lsif-java/src/main/scala/com/sourcegraph/lsif_java/buildtools/GradleBuildTool.scala b/lsif-java/src/main/scala/com/sourcegraph/lsif_java/buildtools/GradleBuildTool.scala
index 9bf98c31..58718a85 100644
--- a/lsif-java/src/main/scala/com/sourcegraph/lsif_java/buildtools/GradleBuildTool.scala
+++ b/lsif-java/src/main/scala/com/sourcegraph/lsif_java/buildtools/GradleBuildTool.scala
@@ -78,7 +78,17 @@ class GradleBuildTool(index: IndexCommand) extends BuildTool("Gradle", index) {
       buildCommand +=
         s"-Porg.gradle.java.installations.paths=${toolchains.paths()}"
     }
-    buildCommand ++= index.finalBuildCommand(List("clean", "compileTestJava"))
+    buildCommand ++=
+      index.finalBuildCommand(
+        List(
+          // Disable the checkerframework plugin because it updates the processorpath
+          // in a way that causes the error "plug-in not found: semanticdb".
+          // Details: https://github.com/kelloggm/checkerframework-gradle-plugin/blob/76d1926ae22144b082dfcfde1abe625750469398/src/main/groovy/org/checkerframework/gradle/plugin/CheckerFrameworkPlugin.groovy#L374-L376
+          "-PskipCheckerFramework",
+          "clean",
+          "compileTestJava"
+        )
+      )
     buildCommand += lsifJavaDependencies
 
     val result = index.process(buildCommand, env = Map("TERM" -> "dumb"))
diff --git a/semanticdb-agent/src/main/java/com/sourcegraph/semanticdb_javac/SemanticdbAgent.java b/semanticdb-agent/src/main/java/com/sourcegraph/semanticdb_javac/SemanticdbAgent.java
index 297d478a..544e79da 100644
--- a/semanticdb-agent/src/main/java/com/sourcegraph/semanticdb_javac/SemanticdbAgent.java
+++ b/semanticdb-agent/src/main/java/com/sourcegraph/semanticdb_javac/SemanticdbAgent.java
@@ -135,12 +135,18 @@ public static void build(
         switch (previousOption) {
           case "-processorpath":
           case "-processor-path":
+          case "-cp":
           case "-classpath":
           case "-class-path":
             isProcessorpathUpdated = true;
             newOptions.add(PLUGINPATH + File.pathSeparator + option);
             break;
+          case "-Xlint":
+            break;
           default:
+            if (option.startsWith("-Xplugin:ErrorProne")) {
+              break;
+            }
             newOptions.add(option);
             break;
         }
@@ -155,13 +161,19 @@ public static void build(
               "-Xplugin:semanticdb -sourceroot:%s -targetroot:%s", SOURCEROOT, TARGETROOT));
 
       if (DEBUGPATH != null) {
-        try (PrintStream fos =
-            new PrintStream(
-                Files.newOutputStream(
-                    Paths.get(DEBUGPATH), StandardOpenOption.APPEND, StandardOpenOption.CREATE))) {
-          fos.println("Java Home: " + System.getProperty("java.home"));
-          fos.println("Old Options: " + arguments);
-          fos.println("New Options: " + newOptions);
+        ArrayList<String> debuglines = new ArrayList<>();
+        debuglines.add("============== Java Home: " + System.getProperty("java.home"));
+        debuglines.add("============== Old Options");
+        debuglines.addAll(arguments);
+        debuglines.add("============== New Options");
+        debuglines.addAll(newOptions);
+
+        try {
+          Files.write(
+              Paths.get(DEBUGPATH),
+              debuglines,
+              StandardOpenOption.CREATE,
+              StandardOpenOption.APPEND);
         } catch (IOException e) {
         }
       }
diff --git a/tests/buildTools/src/test/scala/tests/BaseBuildToolSuite.scala b/tests/buildTools/src/test/scala/tests/BaseBuildToolSuite.scala
index 6cc5ca75..e2e86e1b 100644
--- a/tests/buildTools/src/test/scala/tests/BaseBuildToolSuite.scala
+++ b/tests/buildTools/src/test/scala/tests/BaseBuildToolSuite.scala
@@ -76,7 +76,7 @@ abstract class BaseBuildToolSuite extends MopedSuite(LsifJava.app) {
       if (semanticdbFiles.length != expectedSemanticdbFiles) {
         fail(
           s"Expected $expectedSemanticdbFiles SemanticDB file(s) to be generated.",
-          clues(semanticdbFiles)
+          clues(semanticdbFiles, app.capturedOutput)
         )
       }
       if (expectedPackages.nonEmpty) {
diff --git a/tests/buildTools/src/test/scala/tests/GradleBuildToolSuite.scala b/tests/buildTools/src/test/scala/tests/GradleBuildToolSuite.scala
index f991ac99..8aa5ae0f 100644
--- a/tests/buildTools/src/test/scala/tests/GradleBuildToolSuite.scala
+++ b/tests/buildTools/src/test/scala/tests/GradleBuildToolSuite.scala
@@ -207,4 +207,30 @@ class GradleBuildToolSuite extends BaseBuildToolSuite {
     2, // Two files because `conf/routes` generates a Java file.
     initCommand = gradleVersion("6.8")
   )
+
+  checkBuild(
+    "checkerframework",
+    """|/build.gradle
+       |plugins {
+       |    id 'java'
+       |    id 'org.checkerframework' version '0.5.24'
+       |}
+       |repositories {
+       |    mavenCentral()
+       |}
+       |java {
+       |  toolchain {
+       |    languageVersion = JavaLanguageVersion.of(8)
+       |  }
+       |}
+       |/src/main/java/foo/Example.java
+       |package foo;
+       |public class Example {}
+       |/src/test/java/foo/ExampleSuite.java
+       |package foo;
+       |public class ExampleSuite {}
+       |""".stripMargin,
+    2,
+    initCommand = gradleVersion("6.8.3")
+  )
 }