diff --git a/gradle/libs.versions.toml b/gradle/libs.versions.toml
index d373f86dd..9a52e07f1 100644
--- a/gradle/libs.versions.toml
+++ b/gradle/libs.versions.toml
@@ -16,7 +16,7 @@ junit = "6.0.1"
 nmcp = "1.4.3"
 picocli = "4.7.7"
 protobuf-plugin = "0.9.6"
-protobuf = "3.25.8"
+protobuf = "4.33.2"
 scala-library = "2.12.21"
 scalatest = "3.2.19"
 scalatestplus-junit5 = "3.2.19.0"
diff --git a/isthmus-cli/src/main/java/io/substrait/isthmus/cli/RegisterAtRuntime.java b/isthmus-cli/src/main/java/io/substrait/isthmus/cli/RegisterAtRuntime.java
index 266a36ff0..e39513359 100644
--- a/isthmus-cli/src/main/java/io/substrait/isthmus/cli/RegisterAtRuntime.java
+++ b/isthmus-cli/src/main/java/io/substrait/isthmus/cli/RegisterAtRuntime.java
@@ -1,7 +1,8 @@
 package io.substrait.isthmus.cli;
 
+import com.google.protobuf.DescriptorProtos;
 import com.google.protobuf.Empty;
-import com.google.protobuf.GeneratedMessageV3;
+import com.google.protobuf.GeneratedMessage;
 import com.google.protobuf.MessageLite;
 import com.google.protobuf.ProtocolMessageEnum;
 import io.github.classgraph.ClassGraph;
@@ -54,10 +55,11 @@ public void beforeAnalysis(BeforeAnalysisAccess access) {
 
       // Empty class
       register(Empty.class);
+      registerDeclaredClassesRecursively(DescriptorProtos.class);
 
       try (PackageScanner substrait = new PackageScanner("io.substrait")) {
         // protobuf items
-        substrait.registerByParent(GeneratedMessageV3.class);
+        substrait.registerByParent(GeneratedMessage.class);
         substrait.registerByParent(MessageLite.Builder.class);
         substrait.registerByParent(ProtocolMessageEnum.class);
 
@@ -131,6 +133,13 @@ private static void register(Class<?> c) {
     RuntimeReflection.register(c.getMethods());
   }
 
+  private static void registerDeclaredClassesRecursively(Class<?> c) {
+    register(c);
+    for (Class<?> declaredClass : c.getDeclaredClasses()) {
+      registerDeclaredClassesRecursively(declaredClass);
+    }
+  }
+
   private static final class PackageScanner implements AutoCloseable {
     private final ScanResult scan;