diff --git a/families/openfold3/tests/cpp/fake_build_identity.cpp b/families/openfold3/tests/cpp/fake_build_identity.cpp
new file mode 100644
index 000000000..3a9b524c0
--- /dev/null
+++ b/families/openfold3/tests/cpp/fake_build_identity.cpp
@@ -0,0 +1,8 @@
+/*
+ * SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+extern "C" int openfold3_test_build_id() {
+    return TEST_BUILD_ID;
+}
diff --git a/families/openfold3/tests/cpp/fake_qualification_runtime.cpp b/families/openfold3/tests/cpp/fake_qualification_runtime.cpp
new file mode 100644
index 000000000..3d858ebe7
--- /dev/null
+++ b/families/openfold3/tests/cpp/fake_qualification_runtime.cpp
@@ -0,0 +1,44 @@
+/*
+ * SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+#include "trtmc/openfold3/structure_prediction.h"
+#include "trtmc/runtime/family_loader.h"
+
+#include <dlfcn.h>
+#include <filesystem>
+#include <stdexcept>
+
+extern "C" int openfold3_test_build_id();
+
+namespace {
+
+class Prediction final : public trtmc::openfold3::IStructurePrediction {
+  public:
+    trtmc::openfold3::StructurePredictionResult predict_structure(const std::string&) override {
+        return {"data_test\n", "{\"build_id\":" + std::to_string(TEST_BUILD_ID) + "}"};
+    }
+};
+
+} // namespace
+
+namespace trtmc {
+
+std::unique_ptr<ITask> load_task(const std::string&, const std::string& runtime_root, std::uint64_t,
+                                 const std::string&, bool) {
+    const auto backend = std::filesystem::path(runtime_root) / "libtrtmc_backend_trt.so";
+    void* library = dlopen(backend.c_str(), RTLD_NOW | RTLD_LOCAL);
+    if (library == nullptr)
+        throw std::runtime_error(dlerror());
+    const auto backend_build =
+        reinterpret_cast<int (*)()>(dlsym(library, "openfold3_test_build_id"));
+    const bool matches = backend_build != nullptr && backend_build() == TEST_BUILD_ID &&
+                         openfold3_test_build_id() == TEST_BUILD_ID;
+    dlclose(library);
+    if (!matches)
+        throw std::runtime_error("qualification runtime/core/backend product build mismatch");
+    return std::make_unique<Prediction>();
+}
+
+} // namespace trtmc
diff --git a/families/openfold3/tests/test_e2e.py b/families/openfold3/tests/test_e2e.py
index 3242dbe6a..4e9459f23 100644
--- a/families/openfold3/tests/test_e2e.py
+++ b/families/openfold3/tests/test_e2e.py
@@ -166,6 +166,16 @@ def _run_native(
 ) -> tuple[str, dict]:
     structure = output_root / f"prediction-{index}.cif"
     metadata = output_root / f"prediction-{index}.json"
+    # The qualification executable is built separately from the selected wheel.
+    # Resolve the staged core so copied and symlinked roots both select its
+    # companion loader instead of the executable's source-build RUNPATH.
+    library_root = (runtime_root / "libtrtmc_core.so").resolve(strict=True).parent
+    loader = library_root / "libtrtmc_runtime.so"
+    assert loader.is_file(), f"OpenFold3 runtime is missing its companion loader: {loader}"
+    environment = os.environ.copy()
+    environment["LD_LIBRARY_PATH"] = os.pathsep.join(
+        path for path in (str(library_root), environment.get("LD_LIBRARY_PATH", "")) if path
+    )
     subprocess.run(
         [
             str(qualification),
@@ -177,6 +187,7 @@ def _run_native(
         ],
         check=True,
         timeout=timeout,
+        env=environment,
     )
     return structure.read_text(encoding="utf-8"), json.loads(metadata.read_text(encoding="utf-8"))
 
diff --git a/families/openfold3/tests/test_e2e_runtime.py b/families/openfold3/tests/test_e2e_runtime.py
new file mode 100644
index 000000000..54148637d
--- /dev/null
+++ b/families/openfold3/tests/test_e2e_runtime.py
@@ -0,0 +1,123 @@
+# SPDX-FileCopyrightText: Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
+# SPDX-License-Identifier: Apache-2.0
+
+from __future__ import annotations
+
+import os
+from pathlib import Path
+import shutil
+import subprocess
+
+import pytest
+
+from . import test_e2e as e2e
+
+
+@pytest.fixture(scope="module")
+def qualification_builds(tmp_path_factory):
+    root = tmp_path_factory.mktemp("openfold3-builds")
+    repository = Path(__file__).resolve().parents[3]
+    sources = Path(__file__).with_name("cpp")
+    compiler = shutil.which("c++")
+    assert compiler, "OpenFold3 runtime regression requires a C++ compiler"
+    flags = [
+        compiler,
+        "-std=c++17",
+        f"-I{repository / 'core/runtime/include'}",
+        f"-I{repository / 'families/openfold3/include'}",
+    ]
+    native, wheel = root / "native-build", root / "wheel"
+    for build_id, directory in enumerate((native, wheel), start=1):
+        directory.mkdir()
+        for name in ("core", "backend_trt"):
+            library = f"libtrtmc_{name}.so"
+            subprocess.run(
+                [
+                    *flags,
+                    "-shared",
+                    "-fPIC",
+                    f"-DTEST_BUILD_ID={build_id}",
+                    str(sources / "fake_build_identity.cpp"),
+                    f"-Wl,-soname,{library}",
+                    "-o",
+                    str(directory / library),
+                ],
+                check=True,
+            )
+        subprocess.run(
+            [
+                *flags,
+                "-shared",
+                "-fPIC",
+                f"-DTEST_BUILD_ID={build_id}",
+                str(sources / "fake_qualification_runtime.cpp"),
+                f"-L{directory}",
+                "-ltrtmc_core",
+                "-ldl",
+                "-Wl,-soname,libtrtmc_runtime.so",
+                "-Wl,-rpath,$ORIGIN",
+                "-o",
+                str(directory / "libtrtmc_runtime.so"),
+            ],
+            check=True,
+        )
+    qualification = native / "openfold3_qualification"
+    subprocess.run(
+        [
+            *flags,
+            str(sources / "qualification.cpp"),
+            f"-L{native}",
+            "-ltrtmc_runtime",
+            f"-Wl,-rpath,{native}",
+            f"-Wl,-rpath-link,{native}",
+            "-o",
+            str(qualification),
+        ],
+        check=True,
+    )
+    return qualification, wheel
+
+
+@pytest.mark.parametrize("layout", ("copied", "symlinked"))
+def test_qualification_uses_selected_product_build(
+    qualification_builds, monkeypatch, tmp_path: Path, layout: str
+) -> None:
+    qualification, wheel = qualification_builds
+    runtime_root = tmp_path / "runtime"
+    runtime_root.mkdir()
+    for name in ("libtrtmc_core.so", "libtrtmc_backend_trt.so", "libtrtmc_runtime.so"):
+        if layout == "copied":
+            shutil.copy2(wheel / name, runtime_root / name)
+        elif name != "libtrtmc_runtime.so":
+            (runtime_root / name).symlink_to(wheel / name)
+    # The source-built executable's RUNPATH and the inherited environment both
+    # point at a different product build from the selected wheel libraries.
+    inherited_path = str(qualification.parent)
+    monkeypatch.setenv("LD_LIBRARY_PATH", inherited_path)
+    request = tmp_path / "query.json"
+    request.write_text("{}", encoding="utf-8")
+
+    structure, metadata = e2e._run_native(
+        qualification, runtime_root, tmp_path / "model.bundle", request, tmp_path, 0, 30
+    )
+
+    assert structure == "data_test\n"
+    assert metadata == {"build_id": 2}
+    assert os.environ["LD_LIBRARY_PATH"] == inherited_path
+
+
+def test_qualification_rejects_a_missing_companion_loader(tmp_path: Path) -> None:
+    runtime_root = tmp_path / "runtime"
+    runtime_root.mkdir()
+    (runtime_root / "libtrtmc_core.so").touch()
+
+    with pytest.raises(AssertionError, match="missing its companion loader"):
+        e2e._run_native(
+            tmp_path / "qualification",
+            runtime_root,
+            tmp_path / "model.bundle",
+            tmp_path / "query.json",
+            tmp_path,
+            0,
+            30,
+        )