diff --git a/esphome/components/nrf52/__init__.py b/esphome/components/nrf52/__init__.py
index df86c1693e..9107ff5149 100644
--- a/esphome/components/nrf52/__init__.py
+++ b/esphome/components/nrf52/__init__.py
@@ -963,15 +963,29 @@ def run_compile(args, config: ConfigType) -> bool:
         # so an existing DB is settled, and --cmake-only reconfigures.
         # Sysbuild configures the app image during its own configure, so the
         # app's flags and autoconf.h are settled after this phase too.
-        if not (
-            _app_build_dir(build_dir) / "compile_commands.json"
-        ).is_file() and not run_command_ok(
-            west_cmd + ["--cmake-only", "--", "-DCMAKE_EXPORT_COMPILE_COMMANDS=ON"],
-            env=env,
-            stream_output=True,
-            cwd=str(paths["framework_path"]),
-        ):
-            raise EsphomeError("nRF52 native build failed")
+        if not (_app_build_dir(build_dir) / "compile_commands.json").is_file():
+            if not run_command_ok(
+                west_cmd + ["--cmake-only", "--", "-DCMAKE_EXPORT_COMPILE_COMMANDS=ON"],
+                env=env,
+                stream_output=True,
+                cwd=str(paths["framework_path"]),
+            ):
+                raise EsphomeError("nRF52 native build failed")
+            # The pch includes zephyr/kernel.h, whose syscall headers are
+            # generated at build time (same target the clang-tidy flow uses)
+            if not run_command_ok(
+                [
+                    "cmake",
+                    "--build",
+                    str(_app_build_dir(build_dir)),
+                    "--target",
+                    "zephyr_generated_headers",
+                ],
+                env=env,
+                stream_output=True,
+                cwd=str(paths["framework_path"]),
+            ):
+                raise EsphomeError("nRF52 native build failed")
 
     # An optional speedup must never abort the build
     app_dir = _app_build_dir(build_dir)
diff --git a/tests/unit_tests/components/nrf52/test_pch.py b/tests/unit_tests/components/nrf52/test_pch.py
index 370a5c43ba..ae90570c4a 100644
--- a/tests/unit_tests/components/nrf52/test_pch.py
+++ b/tests/unit_tests/components/nrf52/test_pch.py
@@ -195,7 +195,8 @@ class TestRunCompilePhases:
 
     def test_missing_db_runs_cmake_phase(self, compile_ctx) -> None:
         run_cmd, prepare, build_dir = compile_ctx
-        results = iter([True, False])  # cmake-only ok, final build fails
+        # cmake-only ok, generated headers ok, final build fails
+        results = iter([True, True, False])
 
         def west(cmd, **kwargs):
             # Phase 1 configures the sysbuild app domain
@@ -208,10 +209,22 @@ class TestRunCompilePhases:
         with pytest.raises(EsphomeError, match="nRF52 native build failed"):
             self._run()
         assert "--cmake-only" in run_cmd.call_args_list[0].args[0]
-        assert "--cmake-only" not in run_cmd.call_args_list[1].args[0]
+        # Generated syscall headers are built in the app domain pre-pch
+        headers_cmd = run_cmd.call_args_list[1].args[0]
+        assert headers_cmd[:2] == ["cmake", "--build"]
+        assert str(build_dir / "zephyr") in headers_cmd
+        assert "zephyr_generated_headers" in headers_cmd
+        assert "--cmake-only" not in run_cmd.call_args_list[2].args[0]
         # The pch is prepared in the app domain dir, not the sysbuild root
         assert prepare.call_args.args[0] == build_dir / "zephyr"
 
+    def test_generated_headers_failure_raises(self, compile_ctx) -> None:
+        run_cmd, prepare, _ = compile_ctx
+        run_cmd.side_effect = [True, False]
+        with pytest.raises(EsphomeError, match="nRF52 native build failed"):
+            self._run()
+        assert not prepare.called
+
     def test_cmake_phase_failure_raises(self, compile_ctx) -> None:
         run_cmd, prepare, _ = compile_ctx
         run_cmd.side_effect = [False]
@@ -264,10 +277,10 @@ class TestRunCompilePhases:
     ) -> None:
         run_cmd, prepare, _ = compile_ctx
         prepare.side_effect = RuntimeError("boom")
-        run_cmd.side_effect = [True, False]
+        run_cmd.side_effect = [True, True, False]
         with pytest.raises(EsphomeError, match="nRF52 native build failed"):
             self._run()
-        assert run_cmd.call_count == 2
+        assert run_cmd.call_count == 3
         assert "Precompiled header setup failed" in caplog.text
 
     def test_prepare_failure_strict_raises(
@@ -276,6 +289,6 @@ class TestRunCompilePhases:
         monkeypatch.setenv("ESPHOME_PCH_STRICT", "1")
         run_cmd, prepare, _ = compile_ctx
         prepare.side_effect = RuntimeError("boom")
-        run_cmd.side_effect = [True]
+        run_cmd.side_effect = [True, True]
         with pytest.raises(RuntimeError, match="boom"):
             self._run()