diff --git a/docs/reference/config-reference.rst b/docs/reference/config-reference.rst
index f9c1df4d0..0429c379b 100644
--- a/docs/reference/config-reference.rst
+++ b/docs/reference/config-reference.rst
@@ -26,6 +26,16 @@ For example `flash_attn.yaml`.
 
 .. autopydantic_model:: fromager.packagesettings.SbomSettings
 
+SBOM upstream purls
+^^^^^^^^^^^^^^^^^^^
+
+When ``purl.upstream`` is absent, the upstream SBOM entry identifies the
+resolved source as ``pkg:pypi/<package name>@<resolved version>``. The
+per-package ``purl.name``, ``purl.type``, and ``purl.namespace`` settings and
+the global ``sbom.purl_type`` setting affect the wheel entry only. Previously,
+those settings also changed the upstream entry. Set ``purl.upstream`` to the
+full source purl when the source is not the resolved PyPI package.
+
 Source Resolver
 ^^^^^^^^^^^^^^^
 
diff --git a/src/fromager/packagesettings/_models.py b/src/fromager/packagesettings/_models.py
index 7aa54e0c0..0e6e42a2a 100644
--- a/src/fromager/packagesettings/_models.py
+++ b/src/fromager/packagesettings/_models.py
@@ -115,7 +115,7 @@ class SbomSettings(pydantic.BaseModel):
     """
 
     purl_type: PurlType = "pypi"
-    """Default purl type for all packages (e.g. ``pypi``, ``generic``)"""
+    """Default purl type for wheel package entries (e.g. ``pypi``, ``generic``)"""
 
     repository_url: AnyUrl | None = None
     """Default purl ``repository_url`` qualifier for all packages
@@ -333,9 +333,10 @@ class PurlConfig(pydantic.BaseModel):
     GENERATED_FROM relationship. Used for packages sourced from
     GitHub/GitLab rather than PyPI.
 
-    When absent, the upstream purl keeps the downstream name, type, and
-    namespace but uses the resolved source version instead of a local
-    downstream version override. The ``repository_url`` qualifier is omitted.
+    When absent, the upstream purl is ``pkg:pypi/<package name>@<resolved
+    version>``. Wheel-only name, type, namespace, and version overrides and
+    the global ``sbom.purl_type`` do not change it. For non-PyPI sources,
+    set ``purl.upstream`` explicitly.
     """
 
 
diff --git a/src/fromager/sbom.py b/src/fromager/sbom.py
index 1ce7a4092..1828cf970 100644
--- a/src/fromager/sbom.py
+++ b/src/fromager/sbom.py
@@ -62,26 +62,21 @@ def _build_upstream_purl(
     name: NormalizedName,
     version: Version,
     pbi: PackageBuildInfo,
-    sbom_settings: SbomSettings,
 ) -> PackageURL:
     """Build the upstream source package URL.
 
     If ``upstream`` is set in the per-package ``PurlConfig``, it is
-    used as-is. Otherwise, the upstream purl uses the resolved source
-    version rather than a downstream wheel version override, and excludes
-    the ``repository_url`` qualifier.
+    used as-is. Otherwise, the source is identified by its resolved
+    PyPI name and version, regardless of downstream wheel purl overrides.
     """
     pc = pbi.purl_config
     if pc and pc.upstream:
         return PackageURL.from_string(pc.upstream)
 
-    purl_type = pc.type if pc else None
-    purl_namespace = pc.namespace if pc else None
-    purl_name = pc.name if pc else None
     return PackageURL(
-        type=purl_type or sbom_settings.purl_type,
-        namespace=purl_namespace,
-        name=purl_name or name,
+        type="pypi",
+        namespace=None,
+        name=name,
         version=str(version),
     )
 
@@ -124,7 +119,6 @@ def generate_sbom(
         name=name,
         version=version,
         pbi=pbi,
-        sbom_settings=sbom_settings,
     )
 
     # Derive the document identity from the downstream purl so the
diff --git a/tests/test_sbom.py b/tests/test_sbom.py
index b228c3fba..8e60fee6f 100644
--- a/tests/test_sbom.py
+++ b/tests/test_sbom.py
@@ -4,6 +4,7 @@
 import uuid
 from unittest.mock import patch
 
+import pytest
 from conftest import make_sbom_ctx
 from packaging.requirements import Requirement
 from packaging.version import Version
@@ -174,6 +175,41 @@ def test_generate_sbom_upstream_uses_source_version_without_upstream_override(
     _validate_spdx(doc)
 
 
+@pytest.mark.parametrize(
+    ("package_purl", "sbom_type", "expected_wheel"),
+    [
+        ({"name": "test-pkg-corp"}, "pypi", "pkg:pypi/test-pkg-corp@0.5.5"),
+        ({"type": "generic"}, "pypi", "pkg:generic/test-pkg@0.5.5"),
+        ({"namespace": "acme"}, "pypi", "pkg:pypi/acme/test-pkg@0.5.5"),
+        ({}, "generic", "pkg:generic/test-pkg@0.5.5"),
+    ],
+)
+def test_generate_sbom_upstream_ignores_wheel_purl_overrides(
+    tmp_path: pathlib.Path,
+    package_purl: dict[str, str],
+    sbom_type: str,
+    expected_wheel: str,
+) -> None:
+    """Wheel-only purl settings must not rewrite the source identity."""
+    ctx = make_sbom_ctx(
+        tmp_path,
+        sbom_settings=SbomSettings(purl_type=sbom_type),
+        package_overrides={"purl": package_purl},
+    )
+    doc = sbom.generate_sbom(
+        ctx=ctx,
+        req=Requirement("test-pkg==0.5.5"),
+        version=Version("0.5.5"),
+    )
+
+    wheel, upstream = doc["packages"]
+    assert wheel["externalRefs"][0]["referenceLocator"] == expected_wheel
+    assert upstream["externalRefs"][0]["referenceLocator"] == (
+        "pkg:pypi/test-pkg@0.5.5"
+    )
+    _validate_spdx(doc)
+
+
 def test_generate_sbom_namespace_is_unique_per_document(
     tmp_path: pathlib.Path,
 ) -> None:
@@ -245,9 +281,9 @@ def test_generate_sbom_purl_field_overrides(tmp_path: pathlib.Path) -> None:
     assert wheel["externalRefs"][0]["referenceLocator"] == (
         "pkg:generic/custom-name@1.0.0"
     )
-    # Field overrides carry through to upstream (without qualifiers)
+    # Wheel field overrides must not change the resolved source identity.
     assert upstream["externalRefs"][0]["referenceLocator"] == (
-        "pkg:generic/custom-name@1.0.0"
+        "pkg:pypi/test-pkg@1.0.0"
     )
     # Document identity follows the purl name override
     assert doc["name"] == "custom-name-1.0.0"