diff --git a/javaagent-tooling/src/main/java/io/opentelemetry/javaagent/tooling/instrumentation/InstrumentationModuleInstaller.java b/javaagent-tooling/src/main/java/io/opentelemetry/javaagent/tooling/instrumentation/InstrumentationModuleInstaller.java
index c421cb0f6364..50018051997f 100644
--- a/javaagent-tooling/src/main/java/io/opentelemetry/javaagent/tooling/instrumentation/InstrumentationModuleInstaller.java
+++ b/javaagent-tooling/src/main/java/io/opentelemetry/javaagent/tooling/instrumentation/InstrumentationModuleInstaller.java
@@ -39,6 +39,7 @@
 import java.util.List;
 import java.util.concurrent.atomic.AtomicBoolean;
 import java.util.function.Function;
+import java.util.function.UnaryOperator;
 import net.bytebuddy.agent.builder.AgentBuilder;
 import net.bytebuddy.description.annotation.AnnotationSource;
 import net.bytebuddy.description.type.TypeDescription;
@@ -118,7 +119,17 @@ private AgentBuilder installIndyModule(
           .injectClasses(injectedClassesCollector);
     }
 
-    MuzzleMatcher muzzleMatcher = new MuzzleMatcher(logger, instrumentationModule);
+    MuzzleMatcher muzzleMatcher =
+        new MuzzleMatcher(
+            logger,
+            instrumentationModule,
+            cl ->
+                // In indy modules muzzle searches for types in both application class loader and in
+                // the agent class loader. Since we allow using agent class in indy instrumentation
+                // these classes are treated as regular non-helper classes for which muzzle performs
+                // reference checks.
+                IndyModuleRegistry.createInstrumentationClassLoaderForMuzzle(
+                    instrumentationModule, cl));
 
     Function<ClassLoader, List<HelperClassDefinition>> helperGenerator =
         cl -> {
@@ -187,7 +198,8 @@ private AgentBuilder installInjectingModule(
       return parentAgentBuilder;
     }
 
-    MuzzleMatcher muzzleMatcher = new MuzzleMatcher(logger, instrumentationModule);
+    MuzzleMatcher muzzleMatcher =
+        new MuzzleMatcher(logger, instrumentationModule, UnaryOperator.identity());
     AgentBuilder.Transformer helperInjector =
         new HelperInjector(
             instrumentationModule.instrumentationName(),
diff --git a/javaagent-tooling/src/main/java/io/opentelemetry/javaagent/tooling/instrumentation/MuzzleMatcher.java b/javaagent-tooling/src/main/java/io/opentelemetry/javaagent/tooling/instrumentation/MuzzleMatcher.java
index 2f49e81ff02a..8b70e5ea1f5b 100644
--- a/javaagent-tooling/src/main/java/io/opentelemetry/javaagent/tooling/instrumentation/MuzzleMatcher.java
+++ b/javaagent-tooling/src/main/java/io/opentelemetry/javaagent/tooling/instrumentation/MuzzleMatcher.java
@@ -14,13 +14,12 @@
 import io.opentelemetry.javaagent.tooling.TransformSafeLogger;
 import io.opentelemetry.javaagent.tooling.Utils;
 import io.opentelemetry.javaagent.tooling.config.EarlyInitAgentConfig;
-import io.opentelemetry.javaagent.tooling.instrumentation.indy.IndyModuleRegistry;
-import io.opentelemetry.javaagent.tooling.instrumentation.indy.InstrumentationModuleClassLoader;
 import io.opentelemetry.javaagent.tooling.muzzle.Mismatch;
 import io.opentelemetry.javaagent.tooling.muzzle.ReferenceMatcher;
 import java.security.ProtectionDomain;
 import java.util.List;
 import java.util.concurrent.atomic.AtomicBoolean;
+import java.util.function.UnaryOperator;
 import java.util.logging.Level;
 import java.util.logging.Logger;
 import net.bytebuddy.agent.builder.AgentBuilder;
@@ -38,15 +37,19 @@ class MuzzleMatcher implements AgentBuilder.RawMatcher {
 
   private final TransformSafeLogger instrumentationLogger;
   private final InstrumentationModule instrumentationModule;
+  private final UnaryOperator<ClassLoader> classLoaderTransformer;
   private final Level muzzleLogLevel;
   private final AtomicBoolean initialized = new AtomicBoolean(false);
   private final Cache<ClassLoader, Boolean> matchCache = Cache.weak();
   private volatile ReferenceMatcher referenceMatcher;
 
   MuzzleMatcher(
-      TransformSafeLogger instrumentationLogger, InstrumentationModule instrumentationModule) {
+      TransformSafeLogger instrumentationLogger,
+      InstrumentationModule instrumentationModule,
+      UnaryOperator<ClassLoader> classLoaderTransformer) {
     this.instrumentationLogger = instrumentationLogger;
     this.instrumentationModule = instrumentationModule;
+    this.classLoaderTransformer = classLoaderTransformer;
     this.muzzleLogLevel = EarlyInitAgentConfig.get().isDebug() ? WARNING : FINE;
   }
 
@@ -60,18 +63,7 @@ public boolean matches(
     if (classLoader == BOOTSTRAP_LOADER) {
       classLoader = Utils.getBootstrapProxy();
     }
-    if (instrumentationModule.isIndyModule()) {
-      return matchCache.computeIfAbsent(
-          classLoader,
-          cl -> {
-            InstrumentationModuleClassLoader moduleCl =
-                IndyModuleRegistry.createInstrumentationClassLoaderWithoutRegistration(
-                    instrumentationModule, cl);
-            return doesMatch(moduleCl);
-          });
-    } else {
-      return matchCache.computeIfAbsent(classLoader, this::doesMatch);
-    }
+    return matchCache.computeIfAbsent(classLoaderTransformer.apply(classLoader), this::doesMatch);
   }
 
   private boolean doesMatch(ClassLoader classLoader) {
diff --git a/javaagent-tooling/src/main/java/io/opentelemetry/javaagent/tooling/instrumentation/indy/IndyModuleRegistry.java b/javaagent-tooling/src/main/java/io/opentelemetry/javaagent/tooling/instrumentation/indy/IndyModuleRegistry.java
index 611bf419326e..e28bdde79d49 100644
--- a/javaagent-tooling/src/main/java/io/opentelemetry/javaagent/tooling/instrumentation/indy/IndyModuleRegistry.java
+++ b/javaagent-tooling/src/main/java/io/opentelemetry/javaagent/tooling/instrumentation/indy/IndyModuleRegistry.java
@@ -95,9 +95,8 @@ public static InstrumentationModuleClassLoader getInstrumentationClassLoader(
    * modules from the same module group (see {@link #getModuleGroup(InstrumentationModule)}) will
    * not be installed in this class loader.
    */
-  public static InstrumentationModuleClassLoader
-      createInstrumentationClassLoaderWithoutRegistration(
-          InstrumentationModule module, ClassLoader instrumentedClassLoader) {
+  public static InstrumentationModuleClassLoader createInstrumentationClassLoaderForMuzzle(
+      InstrumentationModule module, ClassLoader instrumentedClassLoader) {
     // TODO: remove this method and replace usages with a custom TypePool implementation instead
     ClassLoader agentOrExtensionCl = module.getClass().getClassLoader();
     InstrumentationModuleClassLoader cl =