diff --git a/buildSrc/src/main/java/com/linecorp/armeria/conventions/spring/SpringBuildUtil.java b/buildSrc/src/main/java/com/linecorp/armeria/conventions/spring/SpringBuildUtil.java
index 6a4019fab45..14e56a182d0 100644
--- a/buildSrc/src/main/java/com/linecorp/armeria/conventions/spring/SpringBuildUtil.java
+++ b/buildSrc/src/main/java/com/linecorp/armeria/conventions/spring/SpringBuildUtil.java
@@ -96,14 +96,16 @@ private static Set<File> sourceDirs(Project project, SourceSetType sourceSetType
             additionalSourceDirs = new String[] {
                     "build/generated/sources/proto/test/grpc",
                     "build/generated/sources/proto/test/java",
-                    "gen-src/test/java"
+                    "gen-src/test/java",
+                    "gen-src/test/javaThrift"
             };
         } else {
             assert sourceSetType == SourceSetType.MAIN;
             additionalSourceDirs = new String[] {
                     "build/generated/sources/proto/main/grpc",
                     "build/generated/sources/proto/main/java",
-                    "gen-src/main/java"
+                    "gen-src/main/java",
+                    "gen-src/main/javaThrift"
             };
         }
         for (String path : additionalSourceDirs) {
diff --git a/gradle/scripts/lib/java-rpc-thrift.gradle b/gradle/scripts/lib/java-rpc-thrift.gradle
index 31f4368aee9..90187ff9151 100644
--- a/gradle/scripts/lib/java-rpc-thrift.gradle
+++ b/gradle/scripts/lib/java-rpc-thrift.gradle
@@ -50,7 +50,10 @@ configure(projectsWithFlags('java')) {
                 includeDirs = [includeDirs]
             }
             includeDirs = project.files(includeDirs)
-            def javaOutputDir = project.file("${project.ext.genSrcDir}/${scope}/java")
+            def javaOutputDir = project.file("${project.ext.genSrcDir}/${scope}/javaThrift")
+            if (!sourceSet.java.srcDirs.contains(javaOutputDir)) {
+                sourceSet.java.srcDir javaOutputDir
+            }
             def jsonOutputDir = project.file("${project.ext.genSrcDir}/${scope}/resources")
             task.configure {
                 // configure inputs and outputs
diff --git a/gradle/scripts/lib/java-shade.gradle b/gradle/scripts/lib/java-shade.gradle
index 140de5873fe..7f0a3810e0a 100644
--- a/gradle/scripts/lib/java-shade.gradle
+++ b/gradle/scripts/lib/java-shade.gradle
@@ -371,7 +371,13 @@ private void configureShadowTask(Project project, ShadowJar task, boolean isMain
 
 
         relocations.each { props ->
-            task.relocate props['from'], props['to']
+            logger.debug("[${project.name}] Relocating ${props['name']} from ${props['from']} to ${props['to']} " +
+                    "in ${isMain ? 'main' : 'test'}")
+            task.relocate(props['from'], props['to']) {
+                exclude {
+                    return isGenerated(project, it.path, isMain)
+                }
+            }
         }
 
         dependencies {
@@ -402,6 +408,34 @@ private void configureShadowTask(Project project, ShadowJar task, boolean isMain
     }
 }
 
+boolean isGenerated(Project project, String path, boolean isMain) {
+    if (path.endsWith("package-info.class")) {
+        return false
+    }
+    if (!path.endsWith('.class')) {
+        return false
+    }
+    // Remove the .class extension.
+    def className = path.substring(0, path.length() - 6)
+    // Remove the inner class part.
+    def topLevelClassName = className.split('\\$')[0]
+
+    def javaSourcePath = "${topLevelClassName}.java"
+    def scope = isMain ? 'main' : 'test'
+    def thriftGenSrcDir = "${project.ext.genSrcDir}/${scope}/javaThrift"
+    def grpcGenSrcDir = "${project.buildDir}/generated/sources/proto/${scope}/grpc"
+    def protoGenSrcDir = "${project.buildDir}/generated/sources/proto/${scope}/java"
+
+    // Check if the source file exists in any of the generated source directories.
+    if (new File("${thriftGenSrcDir}/${javaSourcePath}").exists() ||
+        new File("${grpcGenSrcDir}/${javaSourcePath}").exists() ||
+        new File("${protoGenSrcDir}/${javaSourcePath}").exists()) {
+        logger.debug("[${project.name}] Excluding generated class from shading: ${path}")
+        return true
+    }
+    return false
+}
+
 /**
  * Finds the dependencies of {@code project} recursively and adds the found dependencies to
  * the configuration named as {@code 'shadedJarTestImplementation'}.