diff --git a/platformio/builder/main.py b/platformio/builder/main.py
index 880ca155ac..086bc34777 100644
--- a/platformio/builder/main.py
+++ b/platformio/builder/main.py
@@ -26,6 +26,7 @@
 from SCons.Script import Default  # pylint: disable=import-error
 from SCons.Script import DefaultEnvironment  # pylint: disable=import-error
 from SCons.Script import Import  # pylint: disable=import-error
+from SCons.Script import SetOption  # pylint: disable=import-error
 from SCons.Script import Variables  # pylint: disable=import-error
 
 from platformio import app, fs
@@ -35,6 +36,13 @@
 
 AllowSubstExceptions(NameError)
 
+# SCons normally reuses stored content signatures for files older than its
+# max-drift window when their size and modification time are unchanged. A VCS
+# checkout can replace a source file while preserving both values, which makes
+# the previous object look current. Always calculate dependency signatures from
+# the actual contents so incremental builds cannot mix source states.
+SetOption("max_drift", -1)
+
 # append CLI arguments to build environment
 clivars = Variables(None)
 clivars.AddVariables(
diff --git a/tests/commands/test_run.py b/tests/commands/test_run.py
index 9250b7a6a0..64bfbc4ee2 100644
--- a/tests/commands/test_run.py
+++ b/tests/commands/test_run.py
@@ -12,11 +12,60 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import os
+import subprocess
+import time
 from pathlib import Path
 
 from platformio.run.cli import cli as cmd_run
 
 
+def test_rebuilds_source_when_content_changes_without_metadata_change(
+    clirunner, validate_cliresult, tmp_path: Path
+):
+    project_dir = tmp_path / "project"
+    src_dir = project_dir / "src"
+    src_dir.mkdir(parents=True)
+    (project_dir / "platformio.ini").write_text("""
+[env:native]
+platform = native
+""")
+
+    source_path = src_dir / "main.c"
+    source_path.write_text("int main(void) { return 0; }\n")
+    old_timestamp = time.time() - (3 * 24 * 60 * 60)
+    os.utime(source_path, (old_timestamp, old_timestamp))
+    original_stat = source_path.stat()
+
+    result = clirunner.invoke(cmd_run, ["--project-dir", str(project_dir)])
+    validate_cliresult(result)
+
+    # Reproduce a Git checkout that restores different content with the same
+    # file size and modification time. Timestamp-based SCons deciders otherwise
+    # risk reusing the object produced from the previous source state.
+    source_path.write_text("int main(void) { return 1; }\n")
+    os.utime(
+        source_path,
+        ns=(original_stat.st_atime_ns, original_stat.st_mtime_ns),
+    )
+
+    result = clirunner.invoke(cmd_run, ["--project-dir", str(project_dir)])
+    validate_cliresult(result)
+
+    object_path = project_dir / ".pio" / "build" / "native" / "src" / "main.o"
+    object_mtime_ns = object_path.stat().st_mtime_ns
+
+    program_name = "program.exe" if os.name == "nt" else "program"
+    program_path = project_dir / ".pio" / "build" / "native" / program_name
+    assert subprocess.run([program_path], check=False).returncode == 1
+
+    # Hashing the source again must not turn an unchanged build into a rebuild.
+    time.sleep(0.01)
+    result = clirunner.invoke(cmd_run, ["--project-dir", str(project_dir)])
+    validate_cliresult(result)
+    assert object_path.stat().st_mtime_ns == object_mtime_ns
+
+
 def test_generic_build(clirunner, validate_cliresult, tmpdir):
     build_flags = [
         ("-D TEST_INT=13", "-DTEST_INT=13"),