diff --git a/.github/workflows/cross-platform-test.md b/.github/workflows/cross-platform-test.md
index f1f22f738..5544a4c07 100644
--- a/.github/workflows/cross-platform-test.md
+++ b/.github/workflows/cross-platform-test.md
@@ -160,6 +160,40 @@ test-installation:
       if: steps.install-method.outputs.method == 'wheel'
 ```
 
+## Known Issues
+
+### macOS AMD64 Python 3.13 Compilation Failures
+
+**Issue**: Nightly/release builds may fail on macOS AMD64 with Python 3.13 due to `chroma-hnswlib` compilation errors:
+```
+clang: error: unsupported argument 'native' to option '-march='
+error: command '/usr/bin/clang++' failed with exit code 1
+```
+
+**Root Cause**: Systematic difference in dependency resolution between workspace builds vs published packages:
+
+| Build Type | Package Source | Dependencies | chromadb | Result |
+|------------|----------------|--------------|----------|---------|
+| **Manual/Source** | Workspace (`langflow-base = { workspace = true }`) | 162 packages | ❌ Not included | ✅ Success |
+| **Nightly/Release** | Published (`langflow-base-nightly==0.5.0.dev21`) | 420 packages | ✅ Included | ❌ Compilation fails |
+
+**Technical Details**:
+1. **Workspace builds** use local `src/backend/base/pyproject.toml` which excludes `chromadb`
+2. **Nightly builds** modify dependencies via `scripts/ci/update_uv_dependency.py`:
+   - Changes: `langflow-base~=0.5.0` → `langflow-base-nightly==0.5.0.dev21`
+   - Uses published PyPI package with full dependency tree including `chromadb==0.5.23`
+3. **macOS clang** doesn't support `-march=native` flag used by `chroma-hnswlib` compilation
+
+**Workarounds**:
+- Manual testing (source builds) works consistently
+- Issue only affects nightly/release automated builds
+- Some runs may succeed if compatible `chroma-hnswlib` wheels are available on PyPI
+
+**Files Involved**:
+- `scripts/ci/update_uv_dependency.py` - Modifies dependency resolution
+- `scripts/ci/update_pyproject_combined.py` - Orchestrates nightly build changes
+- `pyproject.toml` vs `src/backend/base/pyproject.toml` - Different dependency trees
+
 ## Results
 
 - ✅ **Success**: All platforms pass installation and basic functionality
diff --git a/.github/workflows/cross-platform-test.yml b/.github/workflows/cross-platform-test.yml
index acbe5e9dd..ffc30d1b8 100644
--- a/.github/workflows/cross-platform-test.yml
+++ b/.github/workflows/cross-platform-test.yml
@@ -217,6 +217,12 @@ jobs:
 
       - name: Install main package from wheel (Unix)
         if: steps.install-method.outputs.method == 'wheel' && matrix.os != 'windows'
+        env:
+          # Fix chroma-hnswlib compilation on macOS by overriding problematic compiler flags
+          CFLAGS: ${{ matrix.os == 'macos' && matrix.python-version == '3.13' && '-O3 -mmacosx-version-min=10.7 -march=x86-64' || '' }}
+          CXXFLAGS: ${{ matrix.os == 'macos' && matrix.python-version == '3.13' && '-O3 -mmacosx-version-min=10.7 -march=x86-64 -stdlib=libc++' || '' }}
+          # Alternative: Force use of compatible architecture flags
+          ARCHFLAGS: ${{ matrix.os == 'macos' && matrix.python-version == '3.13' && '-arch x86_64' || '' }}
         run: |
           ls -la ./main-dist/
           find ./main-dist -name "*.whl" -type f
@@ -242,6 +248,12 @@ jobs:
 
       - name: Install langflow from PyPI (Unix)
         if: steps.install-method.outputs.method == 'pypi' && matrix.os != 'windows'
+        env:
+          # Fix chroma-hnswlib compilation on macOS by overriding problematic compiler flags
+          CFLAGS: ${{ matrix.os == 'macos' && matrix.python-version == '3.13' && '-O3 -mmacosx-version-min=10.7 -march=x86-64' || '' }}
+          CXXFLAGS: ${{ matrix.os == 'macos' && matrix.python-version == '3.13' && '-O3 -mmacosx-version-min=10.7 -march=x86-64 -stdlib=libc++' || '' }}
+          # Alternative: Force use of compatible architecture flags
+          ARCHFLAGS: ${{ matrix.os == 'macos' && matrix.python-version == '3.13' && '-arch x86_64' || '' }}
         run: |
           if [ -n "${{ inputs.langflow-version }}" ]; then
             uv pip install --python ./test-env/bin/python langflow==${{ inputs.langflow-version }}
@@ -278,9 +290,9 @@ jobs:
 
       - name: Test server startup (Windows)
         if: matrix.os == 'windows'
-        timeout-minutes: ${{ inputs.test-timeout }}
+        timeout-minutes: ${{ inputs.test-timeout || 5 }}
         env:
-          TIMEOUT_MINUTES: ${{ inputs.test-timeout }}
+          TIMEOUT_MINUTES: ${{ inputs.test-timeout || 5 }}
         run: |
           # Start server in background
           $serverProcess = Start-Process -FilePath ".\test-env\Scripts\python.exe" -ArgumentList "-m", "langflow", "run", "--host", "localhost", "--port", "7860", "--backend-only" -PassThru -WindowStyle Hidden
@@ -312,9 +324,9 @@ jobs:
 
       - name: Test server startup (Unix)
         if: matrix.os != 'windows'
-        timeout-minutes: ${{ inputs.test-timeout }}
+        timeout-minutes: ${{ inputs.test-timeout || 5 }}
         env:
-          TIMEOUT_MINUTES: ${{ inputs.test-timeout }}
+          TIMEOUT_MINUTES: ${{ inputs.test-timeout || 5 }}
         run: |
           # Start server in background
           ./test-env/bin/python -m langflow run --host localhost --port 7860 --backend-only &