diff --git a/Gems/Atom/gem.json b/Gems/Atom/gem.json
index c74a9013f3..99a715281e 100644
--- a/Gems/Atom/gem.json
+++ b/Gems/Atom/gem.json
@@ -1,3 +1,17 @@
 {
-    "gem_name": "Atom"
+    "gem_name": "Atom",
+    "gem_module_roots": [
+        "Asset/ImageProcessingAtom",
+        "Asset/Shader",
+        "Bootstrap",
+        "Component/DebugCamera",
+        "Feature/Common",
+        "RHI",
+        "RHI/DX12",
+        "RHI/Metal",
+        "RHI/Null",
+        "RHI/Vulkan",
+        "RPI",
+        "Tools/AtomToolsFramework"
+    ]
 }
diff --git a/Gems/AtomLyIntegration/AtomViewportDisplayInfo/gem.json b/Gems/AtomLyIntegration/AtomViewportDisplayInfo/gem.json
deleted file mode 100644
index dd92a99ea9..0000000000
--- a/Gems/AtomLyIntegration/AtomViewportDisplayInfo/gem.json
+++ /dev/null
@@ -1,12 +0,0 @@
-{
-    "gem_name": "AtomLyIntegration_AtomViewportDisplayInfo",
-    "display_name": "Atom Viewport Display Info Overlay",
-    "summary": "Provides a diagnostic viewport overlay for the default O3DE Atom viewport.",
-    "canonical_tags": [
-        "Gem"
-    ],
-    "user_tags": [
-        "AtomLyIntegration",
-        "AtomViewportDisplayInfo"
-    ]
-}
\ No newline at end of file
diff --git a/Gems/AtomLyIntegration/gem.json b/Gems/AtomLyIntegration/gem.json
index 0971ad53c2..c350281ad1 100644
--- a/Gems/AtomLyIntegration/gem.json
+++ b/Gems/AtomLyIntegration/gem.json
@@ -1,3 +1,13 @@
 {
-    "gem_name": "AtomLyIntegration"
+    "gem_name": "AtomLyIntegration",
+    "gem_module_roots": [
+        "AtomBridge",
+        "AtomFont",
+        "AtomImGuiTools",
+        "AtomViewportDisplayInfo",
+        "CommonFeatures",
+        "EMotionFXAtom",
+        "ImguiAtom",
+        "TechnicalArt/DccScriptingInterface"
+    ]
 }