diff --git a/build-tools/automation/azure-pipelines.yaml b/build-tools/automation/azure-pipelines.yaml
index ca669345f15..6d269e1fc73 100644
--- a/build-tools/automation/azure-pipelines.yaml
+++ b/build-tools/automation/azure-pipelines.yaml
@@ -74,7 +74,10 @@ extends:
       binskim:
         scanOutputDirectoryOnly: true
       codeql:
-        runSourceLanguagesInSourceAnalysis: true
+        ${{ if ne(variables['Build.SourceBranch'], 'refs/heads/main') }}:
+          compiled:
+            enabled: false
+            justificationForDisabling: CodeQL disabled for non-main branch builds
       policheck:
         enabled: false
         justification: Built in task does not support multi-language scanning
diff --git a/build-tools/automation/yaml-templates/build-linux.yaml b/build-tools/automation/yaml-templates/build-linux.yaml
index f34a25ba776..796b5fe5df0 100644
--- a/build-tools/automation/yaml-templates/build-linux.yaml
+++ b/build-tools/automation/yaml-templates/build-linux.yaml
@@ -35,6 +35,11 @@ stages:
       CC: gcc-10
     ${{ if eq(parameters.use1ESTemplate, true) }}:
       templateContext:
+        sdl:
+          codeql:
+            compiled:
+              enabled: false
+              justificationForDisabling: CodeQL runs against the Windows build and nightly macOS build
         outputs:
         - output: pipelineArtifact
           displayName: upload linux sdk
diff --git a/build-tools/automation/yaml-templates/build-macos.yaml b/build-tools/automation/yaml-templates/build-macos.yaml
index c279a6752ba..eafc4c7499d 100644
--- a/build-tools/automation/yaml-templates/build-macos.yaml
+++ b/build-tools/automation/yaml-templates/build-macos.yaml
@@ -43,6 +43,11 @@ stages:
       clean: all
     ${{ if eq(parameters.use1ESTemplate, true) }}:
       templateContext:
+        sdl:
+          codeql:
+            compiled:
+              enabled: false
+              justificationForDisabling: CodeQL runs against the Windows build and nightly macOS build
         outputParentDirectory: ${{ parameters.xaSourcePath }}/bin
         outputs:
         - output: pipelineArtifact