diff --git a/conda_lock/conda_lock.py b/conda_lock/conda_lock.py
index 18fef8f0..14af2ac7 100644
--- a/conda_lock/conda_lock.py
+++ b/conda_lock/conda_lock.py
@@ -759,7 +759,7 @@ def create_lockfile_from_spec(
         for dep in deps:
             locked[(dep.manager, dep.name, dep.platform)] = dep
 
-    spec_sources: Dict[str, pathlib.Path] = {}
+    meta_sources: Dict[str, pathlib.Path] = {}
     for source in spec.sources:
         try:
             path = relative_path(lockfile_path.parent, source)
@@ -767,7 +767,7 @@ def create_lockfile_from_spec(
             if "Paths don't have the same drive" not in str(e):
                 raise e
             path = str(source.resolve())
-        spec_sources[path] = source
+        meta_sources[path] = source
 
     if MetadataOption.TimeStamp in metadata_choices:
         time_metadata = TimeMeta.create()
@@ -792,10 +792,10 @@ def create_lockfile_from_spec(
 
     if metadata_choices & {MetadataOption.InputSha, MetadataOption.InputMd5}:
         inputs_metadata: Optional[Dict[str, InputMeta]] = {
-            relative_path: InputMeta.create(
+            meta_src: InputMeta.create(
                 metadata_choices=metadata_choices, src_file=src_file
             )
-            for relative_path, src_file in spec_sources.items()
+            for meta_src, src_file in meta_sources.items()
         }
     else:
         inputs_metadata = None
@@ -808,7 +808,7 @@ def create_lockfile_from_spec(
             content_hash=spec.content_hash(),
             channels=[c for c in spec.channels],
             platforms=spec.platforms,
-            sources=[str(source.resolve()) for source in spec.sources],
+            sources=list(meta_sources.keys()),
             git_metadata=git_metadata,
             time_metadata=time_metadata,
             inputs_metadata=inputs_metadata,
@@ -970,7 +970,11 @@ def run_lock(
             lock_content = parse_conda_lock_file(lockfile_path)
             # reconstruct native paths
             locked_environment_files = [
-                pathlib.Path(
+                pathlib.Path(p)
+                # absolute paths could be locked for both flavours
+                if pathlib.PurePosixPath(p).is_absolute()
+                or pathlib.PureWindowsPath(p).is_absolute()
+                else pathlib.Path(
                     pathlib.PurePosixPath(lockfile_path).parent
                     / pathlib.PurePosixPath(p)
                 )
diff --git a/tests/test-source-paths/sources/environment.yaml b/tests/test-source-paths/sources/environment.yaml
new file mode 100644
index 00000000..97a937a0
--- /dev/null
+++ b/tests/test-source-paths/sources/environment.yaml
@@ -0,0 +1,8 @@
+channels:
+  - conda-forge
+platforms:
+  - linux-64
+dependencies:
+  - python ==3.9.6
+  - pydantic ==1.7
+  - flask <2
diff --git a/tests/test_conda_lock.py b/tests/test_conda_lock.py
index 59719719..337d19d8 100644
--- a/tests/test_conda_lock.py
+++ b/tests/test_conda_lock.py
@@ -921,6 +921,36 @@ def test_run_lock_with_locked_environment_files(
     ]
 
 
+@pytest.fixture
+def source_paths(tmp_path: Path) -> Path:
+    return clone_test_dir("test-source-paths", tmp_path)
+
+
+def test_run_lock_relative_source_path(
+    monkeypatch: "pytest.MonkeyPatch", source_paths: Path, conda_exe: str
+):
+    """run_lock() stores and restores lockfile-relative source paths"""
+    source_paths.joinpath("lockfile").mkdir()
+    monkeypatch.chdir(source_paths)
+    environment = Path("sources/environment.yaml")
+    lockfile = Path("lockfile/conda-lock.yml")
+    run_lock([environment], lockfile_path=lockfile, conda_exe="mamba")
+    lock_content = parse_conda_lock_file(lockfile)
+    locked_environment = lock_content.metadata.sources[0]
+    assert Path(locked_environment) == Path("../sources/environment.yaml")
+    make_lock_files = MagicMock()
+    monkeypatch.setattr("conda_lock.conda_lock.make_lock_files", make_lock_files)
+    run_lock(
+        DEFAULT_FILES, lockfile_path=lockfile, conda_exe=conda_exe, update=["pydantic"]
+    )
+    if sys.version_info < (3, 8):
+        # backwards compat
+        src_files = make_lock_files.call_args_list[0][1]["src_files"]
+    else:
+        src_files = make_lock_files.call_args.kwargs["src_files"]
+    assert [p.resolve() for p in src_files] == [environment.resolve()]
+
+
 def test_run_lock_with_pip(
     monkeypatch: "pytest.MonkeyPatch", pip_environment: Path, conda_exe: str
 ):