diff --git a/mypy/build.py b/mypy/build.py
index 97db8fe1646c..7fc9526ccb2f 100644
--- a/mypy/build.py
+++ b/mypy/build.py
@@ -1030,7 +1030,9 @@ def parse_all(self, states: list[State], post_parse: bool = True) -> None:
 
         parallel_states = []
         for state in states:
-            if not self.fscache.exists(state.xpath, real_only=True):
+            if not self.fscache.exists(state.xpath, real_only=True) or (
+                self.shadow_map and self.maybe_swap_for_shadow_path(state.xpath) != state.xpath
+            ):
                 state.source = state.get_source()
             if state.tree is not None:
                 # The file was already parsed.
diff --git a/test-data/unit/check-incremental.test b/test-data/unit/check-incremental.test
index 9647393cdac6..7ff9fbef06a5 100644
--- a/test-data/unit/check-incremental.test
+++ b/test-data/unit/check-incremental.test
@@ -8139,3 +8139,68 @@ reveal_type(test("int"))
 [out]
 [out2]
 tmp/b.py:2: note: Revealed type is "builtins.int"
+
+[case testIncrementalNativeParserShadowFile]
+# flags: --native-parser --shadow-file tmp/a.py tmp/a_shadow.py
+import a
+import b
+-- a and b don't depend on each other, so they can be checked in parallel.
+[file a.py]
+x: int = 1
+reveal_type(x)
+[file b.py]
+y: int = 2
+[file a_shadow.py]
+x: str = "y"
+reveal_type(x)
+[rechecked]
+[stale]
+[out1]
+tmp/a.py:2: note: Revealed type is "builtins.str"
+[out2]
+tmp/a.py:2: note: Revealed type is "builtins.str"
+
+[case testIncrementalNativeParserShadowFileChanged]
+# flags: --native-parser --shadow-file tmp/a.py tmp/a_shadow.py
+import a
+import b
+-- a and b don't depend on each other, so they can be checked in parallel.
+[file a.py]
+x: int = 1
+reveal_type(x)
+[file b.py]
+y: int = 2
+[file a_shadow.py]
+x: str = "y"
+reveal_type(x)
+[file a_shadow.py.2]
+x: bytes = b"y"
+reveal_type(x)
+[rechecked a]
+[stale a]
+[out1]
+tmp/a.py:2: note: Revealed type is "builtins.str"
+[out2]
+tmp/a.py:2: note: Revealed type is "builtins.bytes"
+
+[case testIncrementalNativeParserShadowFileIntroduced]
+# flags: --native-parser
+# flags2: --native-parser --shadow-file tmp/a.py tmp/a_shadow.py
+import a
+import b
+-- a and b don't depend on each other, so they can be checked in parallel.
+-- The first run has no shadow file; the second run introduces one for a.py.
+[file a.py]
+x: int = 1
+reveal_type(x)
+[file b.py]
+y: int = 2
+[file a_shadow.py.2]
+x: str = "y"
+reveal_type(x)
+[rechecked a]
+[stale a]
+[out1]
+tmp/a.py:2: note: Revealed type is "builtins.int"
+[out2]
+tmp/a.py:2: note: Revealed type is "builtins.str"
diff --git a/test-data/unit/cmdline.test b/test-data/unit/cmdline.test
index cfba7a81e928..7066034b3e39 100644
--- a/test-data/unit/cmdline.test
+++ b/test-data/unit/cmdline.test
@@ -530,6 +530,35 @@ variable has type "bytes")
     b: bytes = 1
                ^
 
+[case testShadowFileWithNativeParser]
+# cmd: mypy --native-parser --shadow-file source.py shadow.py source.py
+[file source.py]
+x: int = 1
+reveal_type(x)
+[file shadow.py]
+x: str = "y"
+reveal_type(x)
+[out]
+source.py:2: note: Revealed type is "str"
+== Return code: 0
+
+[case testShadowFileWithNativeParserParallel]
+# cmd: mypy --native-parser --num-workers=4 --shadow-file a.py a_shadow.py main.py a.py b.py
+[file main.py]
+import a
+import b
+[file a.py]
+x: int = 1
+reveal_type(x)
+[file b.py]
+y: int = 2
+[file a_shadow.py]
+x: str = "y"
+reveal_type(x)
+[out]
+a.py:2: note: Revealed type is "str"
+== Return code: 0
+
 [case testConfigWarnUnusedSection1]
 # cmd: mypy foo.py quux.py spam/eggs.py
 [file mypy.ini]