diff --git a/Lib/test/test_capi/test_config.py b/Lib/test/test_capi/test_config.py
index f10ad50d3bea7e..c750a6c2a477ab 100644
--- a/Lib/test/test_capi/test_config.py
+++ b/Lib/test/test_capi/test_config.py
@@ -356,9 +356,11 @@ def expect_bool_not(value):
                     for value in new_values:
                         expected, expect_flag = expect_func(value)
 
+                        old_flags = sys.flags
                         config_set(name, value)
                         self.assertEqual(config_get(name), expected)
                         self.assertEqual(getattr(sys.flags, sys_flag), expect_flag)
+                        self.assertIsNot(sys.flags, old_flags)
                         if name == "write_bytecode":
                             self.assertEqual(getattr(sys, "dont_write_bytecode"),
                                              expect_flag)
diff --git a/Misc/NEWS.d/next/Core_and_Builtins/2026-06-12-15-30-25.gh-issue-151218.5M_nv8.rst b/Misc/NEWS.d/next/Core_and_Builtins/2026-06-12-15-30-25.gh-issue-151218.5M_nv8.rst
new file mode 100644
index 00000000000000..8183539d9cee93
--- /dev/null
+++ b/Misc/NEWS.d/next/Core_and_Builtins/2026-06-12-15-30-25.gh-issue-151218.5M_nv8.rst
@@ -0,0 +1,3 @@
+:c:func:`PyConfig_Set()` and :func:`sys.set_int_max_str_digits` now replace
+:data:`sys.flags`, instead of modifying :data:`sys.flags` in-place. Patch by
+Victor Stinner.
diff --git a/Python/sysmodule.c b/Python/sysmodule.c
index f7e28086d84fab..aa81d69e97c060 100644
--- a/Python/sysmodule.c
+++ b/Python/sysmodule.c
@@ -1874,7 +1874,8 @@ sys_get_int_max_str_digits_impl(PyObject *module)
 /*[clinic end generated code: output=0042f5e8ae0e8631 input=77fb74e987ba7ecb]*/
 {
     PyInterpreterState *interp = _PyInterpreterState_GET();
-    return PyLong_FromLong(interp->long_state.max_str_digits);
+    int maxdigits = _Py_atomic_load_int(&interp->long_state.max_str_digits);
+    return PyLong_FromLong(maxdigits);
 }
 
 
@@ -3490,14 +3491,50 @@ sys_set_flag(PyObject *flags, Py_ssize_t pos, PyObject *value)
 int
 _PySys_SetFlagObj(Py_ssize_t pos, PyObject *value)
 {
-    PyObject *flags = PySys_GetAttrString("flags");
-    if (flags == NULL) {
-        return -1;
+    PyObject *old_flags = NULL;
+    PyObject *new_flags = NULL;
+    PyObject *flags_str = NULL;
+
+    flags_str = PyUnicode_FromString("flags");
+    if (flags_str == NULL) {
+        goto error;
     }
 
-    sys_set_flag(flags, pos, value);
-    Py_DECREF(flags);
-    return 0;
+    old_flags = PySys_GetAttr(flags_str);
+    if (old_flags == NULL) {
+        goto error;
+    }
+
+    new_flags = PyStructSequence_New(&FlagsType);
+    if (new_flags == NULL) {
+        goto error;
+    }
+
+    for (Py_ssize_t i=0; i < (Py_ssize_t)(Py_ARRAY_LENGTH(flags_fields) - 1); i++) {
+        if (i != pos) {
+            PyObject *old_value;
+            old_value = PyStructSequence_GET_ITEM(old_flags, i);  // borrowed ref
+            if (old_value == NULL) {
+                goto error;
+            }
+            sys_set_flag(new_flags, i, old_value);
+        }
+        else {
+            sys_set_flag(new_flags, pos, value);
+        }
+    }
+
+    int res = _PySys_SetAttr(flags_str, new_flags);
+    Py_DECREF(flags_str);
+    Py_DECREF(old_flags);
+    Py_DECREF(new_flags);
+    return res;
+
+error:
+    Py_DECREF(flags_str);
+    Py_DECREF(old_flags);
+    Py_DECREF(new_flags);
+    return -1;
 }
 
 
@@ -3521,8 +3558,6 @@ set_flags_from_config(PyInterpreterState *interp, PyObject *flags)
     const PyPreConfig *preconfig = &interp->runtime->preconfig;
     const PyConfig *config = _PyInterpreterState_GetConfig(interp);
 
-    // _PySys_UpdateConfig() modifies sys.flags in-place:
-    // Py_XDECREF() is needed in this case.
     Py_ssize_t pos = 0;
 #define SetFlagObj(expr) \
     do { \
@@ -4153,16 +4188,27 @@ _PySys_UpdateConfig(PyThreadState *tstate)
 #undef COPY_LIST
 #undef COPY_WSTR
 
-    // sys.flags
-    PyObject *flags = PySys_GetAttrString("flags");
-    if (flags == NULL) {
+    // replace sys.flags
+    PyObject *new_flags = PyStructSequence_New(&FlagsType);
+    if (new_flags == NULL) {
         return -1;
     }
-    if (set_flags_from_config(interp, flags) < 0) {
-        Py_DECREF(flags);
+    if (set_flags_from_config(interp, new_flags) < 0) {
+        Py_DECREF(new_flags);
+        return -1;
+    }
+
+    PyObject *flags_str = PyUnicode_FromString("flags");
+    if (flags_str == NULL) {
+        Py_DECREF(new_flags);
+        return -1;
+    }
+    res = _PySys_SetAttr(flags_str, new_flags);
+    Py_DECREF(new_flags);
+    Py_DECREF(flags_str);
+    if (res < 0) {
         return -1;
     }
-    Py_DECREF(flags);
 
     SET_SYS("dont_write_bytecode", PyBool_FromLong(!config->write_bytecode));
 
@@ -4675,7 +4721,7 @@ _PySys_SetIntMaxStrDigits(int maxdigits)
     // Set PyInterpreterState.long_state.max_str_digits
     // and PyInterpreterState.config.int_max_str_digits.
     PyInterpreterState *interp = _PyInterpreterState_GET();
-    interp->long_state.max_str_digits = maxdigits;
-    interp->config.int_max_str_digits = maxdigits;
+    _Py_atomic_store_int(&interp->long_state.max_str_digits, maxdigits);
+    _Py_atomic_store_int(&interp->config.int_max_str_digits, maxdigits);
     return 0;
 }