diff --git a/src/main/groovy/org/inferred/gradle/ProcessorsPlugin.groovy b/src/main/groovy/org/inferred/gradle/ProcessorsPlugin.groovy
index 49c95ee0..8614cfb3 100644
--- a/src/main/groovy/org/inferred/gradle/ProcessorsPlugin.groovy
+++ b/src/main/groovy/org/inferred/gradle/ProcessorsPlugin.groovy
@@ -111,15 +111,17 @@ class ProcessorsPlugin implements Plugin<Project> {
       })
     })
 
-    // If the project uses .idea directory structure, update compiler.xml directly
-    File ideaCompilerXml = project.file('.idea/compiler.xml')
-    if (ideaCompilerXml.isFile()) {
-      Node parsedProjectXml = (new XmlParser()).parse(ideaCompilerXml)
-      updateIdeaCompilerConfiguration(project, parsedProjectXml)
-      ideaCompilerXml.withWriter { writer ->
-        XmlNodePrinter nodePrinter = new XmlNodePrinter(new PrintWriter(writer))
-        nodePrinter.setPreserveWhitespace(true)
-        nodePrinter.print(parsedProjectXml)
+    project.afterEvaluate {
+      // If the project uses .idea directory structure, update compiler.xml directly
+      File ideaCompilerXml = project.file('.idea/compiler.xml')
+      if (ideaCompilerXml.isFile()) {
+        Node parsedProjectXml = (new XmlParser()).parse(ideaCompilerXml)
+        updateIdeaCompilerConfiguration(project, parsedProjectXml)
+        ideaCompilerXml.withWriter { writer ->
+          XmlNodePrinter nodePrinter = new XmlNodePrinter(new PrintWriter(writer))
+          nodePrinter.setPreserveWhitespace(true)
+          nodePrinter.print(parsedProjectXml)
+        }
       }
     }
 
@@ -203,11 +205,18 @@ class ProcessorsPlugin implements Plugin<Project> {
       new Node(compilerConfiguration, "annotationProcessing")
     }
 
+    def outputDir = 'generated_src'
+    def testOutputDir = 'generated_testSrc'
+    if (project.hasProperty('idea')) {
+      outputDir = project.idea.processors.outputDir
+      testOutputDir = project.idea.processors.testOutputDir
+    }
+
     compilerConfiguration.annotationProcessing.replaceNode{
       annotationProcessing() {
         profile(default: 'true', name: 'Default', enabled: 'true') {
-          sourceOutputDir(name: project.idea.processors.outputDir)
-          sourceTestOutputDir(name: project.idea.processors.testOutputDir)
+          sourceOutputDir(name: outputDir)
+          sourceTestOutputDir(name: testOutputDir)
           outputRelativeToContentRoot(value: 'true')
           processorPath(useClasspath: 'true')
         }
diff --git a/src/test/groovy/org/inferred/gradle/ProcessorsPluginFunctionalTest.groovy b/src/test/groovy/org/inferred/gradle/ProcessorsPluginFunctionalTest.groovy
index d3875454..aac01f85 100644
--- a/src/test/groovy/org/inferred/gradle/ProcessorsPluginFunctionalTest.groovy
+++ b/src/test/groovy/org/inferred/gradle/ProcessorsPluginFunctionalTest.groovy
@@ -657,6 +657,54 @@ public class ProcessorsPluginFunctionalTest {
     assertEquals(expected, xml)
   }
 
+  @Test
+  public void testUserSpecifiedDirectoriesUsedInIdeaCompilerXml() throws IOException {
+    buildFile << """
+      apply plugin: 'java'
+      apply plugin: 'idea'
+      apply plugin: 'org.inferred.processors'
+
+      idea.processors {
+        outputDir = 'foo'
+        testOutputDir = 'bar'
+      }
+    """
+
+    new File(testProjectDir.newFolder('.idea'), 'compiler.xml') << """
+      <?xml version="1.0" encoding="UTF-8"?>
+      <project version="4">
+        <component name="CompilerConfiguration">
+          <annotationProcessing/>
+        </component>
+      </project>
+    """.trim()
+
+    File testProjectDirRoot = testProjectDir.getRoot()
+    GradleRunner.create()
+            .withProjectDir(testProjectDirRoot)
+            .withArguments("idea", "--stacktrace")
+            .build()
+
+    def xml = testProjectDirRoot.toPath().resolve(".idea/compiler.xml").toFile().text.trim()
+
+    def expected = """
+      <project version="4">
+        <component name="CompilerConfiguration">
+          <annotationProcessing>
+            <profile default="true" name="Default" enabled="true">
+              <sourceOutputDir name="foo"/>
+              <sourceTestOutputDir name="bar"/>
+              <outputRelativeToContentRoot value="true"/>
+              <processorPath useClasspath="true"/>
+            </profile>
+          </annotationProcessing>
+        </component>
+      </project>
+    """.stripIndent().trim()
+
+    assertEquals(expected, xml)
+  }
+
   @Test
   public void testOnlyApplyToSubProject() {
     testProjectDir.newFolder("projectA")
@@ -745,6 +793,98 @@ public class ProcessorsPluginFunctionalTest {
     assertAutoValueInFile(new File(runner.projectDir, ".factorypath"))
   }
 
+  /** @see https://github.com/palantir/gradle-processors/issues/28 */
+  @Test
+  public void testIdeaCompilerConfigurationUpdatedWithoutNeedToApplyIdeaPlugin() throws IOException {
+    buildFile << """
+      apply plugin: 'java'
+      apply plugin: 'org.inferred.processors'
+    """
+
+    new File(testProjectDir.newFolder('.idea'), 'compiler.xml') << """
+      <?xml version="1.0" encoding="UTF-8"?>
+      <project version="4">
+        <component name="CompilerConfiguration">
+          <annotationProcessing/>
+        </component>
+      </project>
+    """.trim()
+
+    File testProjectDirRoot = testProjectDir.getRoot()
+    GradleRunner.create()
+            .withProjectDir(testProjectDirRoot)
+            .withArguments("tasks", "--stacktrace")
+            .build()
+
+    def xml = testProjectDirRoot.toPath().resolve(".idea/compiler.xml").toFile().text.trim()
+
+    def expected = """
+      <project version="4">
+        <component name="CompilerConfiguration">
+          <annotationProcessing>
+            <profile default="true" name="Default" enabled="true">
+              <sourceOutputDir name="generated_src"/>
+              <sourceTestOutputDir name="generated_testSrc"/>
+              <outputRelativeToContentRoot value="true"/>
+              <processorPath useClasspath="true"/>
+            </profile>
+          </annotationProcessing>
+        </component>
+      </project>
+    """.stripIndent().trim()
+
+    assertEquals(expected, xml)
+  }
+
+  /** @see https://github.com/palantir/gradle-processors/issues/53 */
+  @Test
+  public void testCompilerXmlModificationWhenIdeaPluginImportedLast() throws IOException {
+    buildFile << """
+      apply plugin: 'java'
+      apply plugin: 'org.inferred.processors'
+      apply plugin: 'idea'
+
+      idea.processors {
+        outputDir = 'foo'
+        testOutputDir = 'bar'
+      }
+    """
+
+    new File(testProjectDir.newFolder('.idea'), 'compiler.xml') << """
+      <?xml version="1.0" encoding="UTF-8"?>
+      <project version="4">
+        <component name="CompilerConfiguration">
+          <annotationProcessing/>
+        </component>
+      </project>
+    """.trim()
+
+    File testProjectDirRoot = testProjectDir.getRoot()
+    GradleRunner.create()
+            .withProjectDir(testProjectDirRoot)
+            .withArguments("idea", "--stacktrace")
+            .build()
+
+    def xml = testProjectDirRoot.toPath().resolve(".idea/compiler.xml").toFile().text.trim()
+
+    def expected = """
+      <project version="4">
+        <component name="CompilerConfiguration">
+          <annotationProcessing>
+            <profile default="true" name="Default" enabled="true">
+              <sourceOutputDir name="foo"/>
+              <sourceTestOutputDir name="bar"/>
+              <outputRelativeToContentRoot value="true"/>
+              <processorPath useClasspath="true"/>
+            </profile>
+          </annotationProcessing>
+        </component>
+      </project>
+    """.stripIndent().trim()
+
+    assertEquals(expected, xml)
+  }
+
   private void assertAutoValueInFile(File file) {
     if (!file.any { it.contains("auto-value-1.0.jar") }) {
       println "====== $file.name ============================================================"