diff --git a/mypy/config_parser.py b/mypy/config_parser.py
index a6bf021000c1..c44a4cda24ba 100644
--- a/mypy/config_parser.py
+++ b/mypy/config_parser.py
@@ -231,7 +231,7 @@ def split_commas(value: str) -> list[str]:
 
 def parse_config_file(
     options: Options,
-    set_strict_flags: Callable[[], None],
+    strict_flag_assignments: Sequence[tuple[str, object]],
     filename: str | None,
     stdout: TextIO | None = None,
     stderr: TextIO | None = None,
@@ -284,6 +284,9 @@ def parse_config_file(
 
     os.environ["MYPY_CONFIG_FILE_DIR"] = os.path.dirname(os.path.abspath(config_file))
 
+    def set_strict_flags(updates: dict[str, object]) -> None:
+        updates.update(strict_flag_assignments)
+
     if "mypy" not in parser:
         if filename or file_read not in defaults.SHARED_CONFIG_FILES:
             print(f"{file_read}: No [mypy] section in config file", file=stderr)
@@ -297,11 +300,16 @@ def parse_config_file(
             setattr(options, k, v)
         options.report_dirs.update(report_dirs)
 
+    def set_strict_flags_section(updates: dict[str, object]) -> None:
+        for dest, value in strict_flag_assignments:
+            if dest in PER_MODULE_OPTIONS:
+                updates[dest] = value
+
     for name, section in parser.items():
         if name.startswith("mypy-"):
             prefix = get_prefix(file_read, name)
             updates, report_dirs = parse_section(
-                prefix, options, set_strict_flags, section, config_types, stderr
+                prefix, options, set_strict_flags_section, section, config_types, stderr
             )
             if report_dirs:
                 print(
@@ -440,7 +448,7 @@ def destructure_overrides(toml_data: dict[str, Any]) -> dict[str, Any]:
 def parse_section(
     prefix: str,
     template: Options,
-    set_strict_flags: Callable[[], None],
+    set_strict_flags: Callable[[dict[str, object]], None],
     section: Mapping[str, Any],
     config_types: dict[str, Any],
     stderr: TextIO = sys.stderr,
@@ -535,7 +543,7 @@ def parse_section(
             continue
         if key == "strict":
             if v:
-                set_strict_flags()
+                set_strict_flags(results)
             continue
         results[options_key] = v
 
@@ -631,7 +639,7 @@ def parse_mypy_comments(
         stderr = StringIO()
         strict_found = False
 
-        def set_strict_flags() -> None:
+        def set_strict_flags(updates: dict[str, object]) -> None:
             nonlocal strict_found
             strict_found = True
 
diff --git a/mypy/main.py b/mypy/main.py
index ae3e7d75be7f..7616bbc4468d 100644
--- a/mypy/main.py
+++ b/mypy/main.py
@@ -1265,21 +1265,15 @@ def add_invertible_flag(
         parser.error(f"Cannot find config file '{config_file}'")
 
     options = Options()
-    strict_option_set = False
-
-    def set_strict_flags() -> None:
-        nonlocal strict_option_set
-        strict_option_set = True
-        for dest, value in strict_flag_assignments:
-            setattr(options, dest, value)
 
     # Parse config file first, so command line can override.
-    parse_config_file(options, set_strict_flags, config_file, stdout, stderr)
+    parse_config_file(options, strict_flag_assignments, config_file, stdout, stderr)
 
     # Set strict flags before parsing (if strict mode enabled), so other command
     # line options can override.
     if getattr(dummy, "special-opts:strict"):
-        set_strict_flags()
+        for dest, value in strict_flag_assignments:
+            setattr(options, dest, value)
 
     # Override cache_dir if provided in the environment
     environ_cache_dir = os.getenv("MYPY_CACHE_DIR", "")
@@ -1400,9 +1394,6 @@ def set_strict_flags() -> None:
             " new type inference algorithm is already enabled by default"
         )
 
-    if options.strict_concatenate and not strict_option_set:
-        print("Warning: --strict-concatenate is deprecated; use --extra-checks instead")
-
     # Set target.
     if special_opts.modules + special_opts.packages:
         options.build_type = BuildType.MODULE
diff --git a/mypy/options.py b/mypy/options.py
index d315d297e023..e869781d9537 100644
--- a/mypy/options.py
+++ b/mypy/options.py
@@ -212,7 +212,7 @@ def __init__(self) -> None:
         # This makes 1 == '1', 1 in ['1'], and 1 is '1' errors.
         self.strict_equality = False
 
-        # Deprecated, use extra_checks instead.
+        # Make arguments prepended via Concatenate be truly positional-only.
         self.strict_concatenate = False
 
         # Enable additional checks that are technically correct but impractical.
diff --git a/mypy/stubtest.py b/mypy/stubtest.py
index 36cd0a213d4d..b91466e6a9f5 100644
--- a/mypy/stubtest.py
+++ b/mypy/stubtest.py
@@ -1940,15 +1940,12 @@ def test_stubs(args: _Arguments, use_builtins_fixtures: bool = False) -> int:
         options.abs_custom_typeshed_dir = os.path.abspath(options.custom_typeshed_dir)
     options.config_file = args.mypy_config_file
     options.use_builtins_fixtures = use_builtins_fixtures
+    options.per_module_options = {}
     options.show_traceback = args.show_traceback
     options.pdb = args.pdb
 
     if options.config_file:
-
-        def set_strict_flags() -> None:  # not needed yet
-            return
-
-        parse_config_file(options, set_strict_flags, options.config_file, sys.stdout, sys.stderr)
+        parse_config_file(options, [], options.config_file, sys.stdout, sys.stderr)
 
     def error_callback(msg: str) -> typing.NoReturn:
         print(_style("error:", color="red", bold=True), msg)
diff --git a/mypy/test/testfinegrained.py b/mypy/test/testfinegrained.py
index 800ba2dff087..0f86e7c20dae 100644
--- a/mypy/test/testfinegrained.py
+++ b/mypy/test/testfinegrained.py
@@ -162,7 +162,7 @@ def get_options(self, source: str, testcase: DataDrivenTestCase, build_cache: bo
 
         for name, _ in testcase.files:
             if "mypy.ini" in name or "pyproject.toml" in name:
-                parse_config_file(options, lambda: None, name)
+                parse_config_file(options, [], name)
                 break
 
         return options
diff --git a/test-data/unit/check-flags.test b/test-data/unit/check-flags.test
index c6419923ebc6..6219082171df 100644
--- a/test-data/unit/check-flags.test
+++ b/test-data/unit/check-flags.test
@@ -2125,6 +2125,31 @@ disallow_subclassing_any = true
 module = 'm'
 disallow_subclassing_any = false
 
+[case testStrictPerModule]
+# flags: --config-file tmp/mypy.ini
+
+import strictmodule
+import loosemodule
+a = 0  # type: ignore
+
+[file strictmodule.py]
+def foo():  # E: Function is missing a return type annotation \
+            # N: Use "-> None" if function does not return a value
+    1 + "asdf"  # E: Unsupported operand types for + ("int" and "str")
+
+a = 0  # type: ignore  # E: Unused "type: ignore" comment
+
+[file loosemodule.py]
+def foo():
+    1 + "asdf"
+
+a = 0  # type: ignore
+
+[file mypy.ini]
+\[mypy]
+strict = False
+\[mypy-strictmodule]
+strict = True
 
 [case testNoImplicitOptionalPerModule]
 # flags: --config-file tmp/mypy.ini