diff --git a/pandas/core/arrays/arrow/dtype.py b/pandas/core/arrays/arrow/dtype.py
index 90c86cd6d55ef..437cd975b6bb2 100644
--- a/pandas/core/arrays/arrow/dtype.py
+++ b/pandas/core/arrays/arrow/dtype.py
@@ -4,6 +4,7 @@
 
 import numpy as np
 
+from pandas._libs import missing as libmissing
 from pandas._typing import (
     TYPE_CHECKING,
     DtypeObj,
@@ -209,6 +210,9 @@ def _get_common_dtype(self, dtypes: list[DtypeObj]) -> DtypeObj | None:
         except NotImplementedError:
             return None
 
+    def _is_valid_na_for_dtype(self, value) -> bool:
+        return value is None or value is libmissing.NA
+
     def __from_arrow__(self, array: pa.Array | pa.ChunkedArray):
         """
         Construct IntegerArray/FloatingArray from pyarrow Array/ChunkedArray.
diff --git a/pandas/core/arrays/base.py b/pandas/core/arrays/base.py
index c261a41e1e77e..6d0ff112ad235 100644
--- a/pandas/core/arrays/base.py
+++ b/pandas/core/arrays/base.py
@@ -425,7 +425,7 @@ def __contains__(self, item: object) -> bool | np.bool_:
         if is_scalar(item) and isna(item):
             if not self._can_hold_na:
                 return False
-            elif item is self.dtype.na_value or isinstance(item, self.dtype.type):
+            elif self.dtype._is_valid_na_for_dtype(item):
                 return self._hasna
             else:
                 return False
diff --git a/pandas/core/dtypes/base.py b/pandas/core/dtypes/base.py
index bce2a82f057f3..b8f117b8ef547 100644
--- a/pandas/core/dtypes/base.py
+++ b/pandas/core/dtypes/base.py
@@ -61,9 +61,11 @@ class ExtensionDtype:
     * _is_numeric
     * _is_boolean
     * _get_common_dtype
+    * _is_valid_na_for_dtype
 
     The `na_value` class attribute can be used to set the default NA value
-    for this type. :attr:`numpy.nan` is used by default.
+    for this type. :attr:`numpy.nan` is used by default. What other NA values
+    are accepted can be fine-tuned by overriding ``_is_valid_na_for_dtype``.
 
     ExtensionDtypes are required to be hashable. The base class provides
     a default implementation, which relies on the ``_metadata`` class
@@ -390,6 +392,26 @@ def _can_hold_na(self) -> bool:
         """
         return True
 
+    def _is_valid_na_for_dtype(self, value) -> bool:
+        """
+        Should we treat this value as interchangeable with self.na_value?
+
+        Use cases include:
+
+        - series[key] = value
+        - series.replace(other, value)
+        - value in index
+
+        If ``value`` is a valid na for this dtype, ``self.na_value`` will be used
+        in its place for the purpose of this operations.
+
+        Notes
+        -----
+        The base class implementation considers any scalar recognized by pd.isna
+        to be equivalent.
+        """
+        return libmissing.checknull(value)
+
 
 class StorageExtensionDtype(ExtensionDtype):
     """ExtensionDtype that may be backed by more than one implementation."""
diff --git a/pandas/core/dtypes/dtypes.py b/pandas/core/dtypes/dtypes.py
index 33ff6d1eee686..1d3221f23fd4a 100644
--- a/pandas/core/dtypes/dtypes.py
+++ b/pandas/core/dtypes/dtypes.py
@@ -3,6 +3,7 @@
 """
 from __future__ import annotations
 
+from decimal import Decimal
 import re
 from typing import (
     TYPE_CHECKING,
@@ -14,7 +15,10 @@
 import numpy as np
 import pytz
 
-from pandas._libs import missing as libmissing
+from pandas._libs import (
+    lib,
+    missing as libmissing,
+)
 from pandas._libs.interval import Interval
 from pandas._libs.properties import cache_readonly
 from pandas._libs.tslibs import (
@@ -629,6 +633,11 @@ def _get_common_dtype(self, dtypes: list[DtypeObj]) -> DtypeObj | None:
 
         return find_common_type(non_cat_dtypes)
 
+    def _is_valid_na_for_dtype(self, value) -> bool:
+        from pandas.core.dtypes.missing import is_valid_na_for_dtype
+
+        return is_valid_na_for_dtype(value, self.categories.dtype)
+
 
 @register_extension_dtype
 class DatetimeTZDtype(PandasExtensionDtype):
@@ -819,6 +828,10 @@ def __setstate__(self, state) -> None:
         self._tz = state["tz"]
         self._unit = state["unit"]
 
+    def _is_valid_na_for_dtype(self, value) -> bool:
+        # we have to rule out tznaive dt64("NaT")
+        return not isinstance(value, (np.timedelta64, np.datetime64, Decimal))
+
 
 @register_extension_dtype
 class PeriodDtype(PeriodDtypeBase, PandasExtensionDtype):
@@ -1036,6 +1049,9 @@ def __from_arrow__(
             return PeriodArray(np.array([], dtype="int64"), freq=self.freq, copy=False)
         return PeriodArray._concat_same_type(results)
 
+    def _is_valid_na_for_dtype(self, value) -> bool:
+        return not isinstance(value, (np.datetime64, np.timedelta64, Decimal))
+
 
 @register_extension_dtype
 class IntervalDtype(PandasExtensionDtype):
@@ -1304,6 +1320,9 @@ def _get_common_dtype(self, dtypes: list[DtypeObj]) -> DtypeObj | None:
             return np.dtype(object)
         return IntervalDtype(common, closed=closed)
 
+    def _is_valid_na_for_dtype(self, value) -> bool:
+        return lib.is_float(value) or value is None or value is libmissing.NA
+
 
 class PandasDtype(ExtensionDtype):
     """
@@ -1479,3 +1498,6 @@ def _get_common_dtype(self, dtypes: list[DtypeObj]) -> DtypeObj | None:
             return type(self).from_numpy_dtype(new_dtype)
         except (KeyError, NotImplementedError):
             return None
+
+    def _is_valid_na_for_dtype(self, value) -> bool:
+        return value is None or value is libmissing.NA
diff --git a/pandas/core/dtypes/missing.py b/pandas/core/dtypes/missing.py
index 211b67d3590ed..f111bd97a00de 100644
--- a/pandas/core/dtypes/missing.py
+++ b/pandas/core/dtypes/missing.py
@@ -38,10 +38,8 @@
     needs_i8_conversion,
 )
 from pandas.core.dtypes.dtypes import (
-    CategoricalDtype,
     DatetimeTZDtype,
     ExtensionDtype,
-    IntervalDtype,
     PeriodDtype,
 )
 from pandas.core.dtypes.generic import (
@@ -692,40 +690,33 @@ def is_valid_na_for_dtype(obj, dtype: DtypeObj) -> bool:
     """
     if not lib.is_scalar(obj) or not isna(obj):
         return False
-    elif dtype.kind == "M":
-        if isinstance(dtype, np.dtype):
+
+    elif isinstance(dtype, np.dtype):
+        if dtype.kind == "M":
             # i.e. not tzaware
             return not isinstance(obj, (np.timedelta64, Decimal))
-        # we have to rule out tznaive dt64("NaT")
-        return not isinstance(obj, (np.timedelta64, np.datetime64, Decimal))
-    elif dtype.kind == "m":
-        return not isinstance(obj, (np.datetime64, Decimal))
-    elif dtype.kind in ["i", "u", "f", "c"]:
-        # Numeric
-        return obj is not NaT and not isinstance(obj, (np.datetime64, np.timedelta64))
-    elif dtype.kind == "b":
-        # We allow pd.NA, None, np.nan in BooleanArray (same as IntervalDtype)
-        return lib.is_float(obj) or obj is None or obj is libmissing.NA
-
-    elif dtype == _dtype_str:
-        # numpy string dtypes to avoid float np.nan
-        return not isinstance(obj, (np.datetime64, np.timedelta64, Decimal, float))
-
-    elif dtype == _dtype_object:
-        # This is needed for Categorical, but is kind of weird
-        return True
-
-    elif isinstance(dtype, PeriodDtype):
-        return not isinstance(obj, (np.datetime64, np.timedelta64, Decimal))
-
-    elif isinstance(dtype, IntervalDtype):
-        return lib.is_float(obj) or obj is None or obj is libmissing.NA
+        elif dtype.kind == "m":
+            return not isinstance(obj, (np.datetime64, Decimal))
+        elif dtype.kind in ["i", "u", "f", "c"]:
+            # Numeric
+            return obj is not NaT and not isinstance(
+                obj, (np.datetime64, np.timedelta64)
+            )
+        elif dtype == _dtype_str:
+            # numpy string dtypes to avoid float np.nan
+            return not isinstance(obj, (np.datetime64, np.timedelta64, Decimal, float))
+        elif dtype == _dtype_object:
+            # This is needed for Categorical, but is kind of weird
+            return True
+        elif dtype.kind == "b":
+            # We allow pd.NA, None, np.nan in BooleanArray (same as IntervalDtype)
+            return lib.is_float(obj) or obj is None or obj is libmissing.NA
 
-    elif isinstance(dtype, CategoricalDtype):
-        return is_valid_na_for_dtype(obj, dtype.categories.dtype)
+        # fallback, default to allowing NaN, None, NA, NaT
+        return not isinstance(obj, (np.datetime64, np.timedelta64, Decimal))
 
-    # fallback, default to allowing NaN, None, NA, NaT
-    return not isinstance(obj, (np.datetime64, np.timedelta64, Decimal))
+    else:
+        return dtype._is_valid_na_for_dtype(obj)
 
 
 def isna_all(arr: ArrayLike) -> bool:
diff --git a/pandas/core/generic.py b/pandas/core/generic.py
index cb321f0584294..7807f0a170bd1 100644
--- a/pandas/core/generic.py
+++ b/pandas/core/generic.py
@@ -35,7 +35,10 @@
     using_copy_on_write,
 )
 
-from pandas._libs import lib
+from pandas._libs import (
+    lib,
+    missing as libmissing,
+)
 from pandas._libs.lib import is_range_indexer
 from pandas._libs.tslibs import (
     Period,
@@ -8012,7 +8015,7 @@ def _clip_with_scalar(self, lower, upper, inplace: bool_t = False):
                 result = result.where(subset, lower, axis=None, inplace=False)
 
         if np.any(mask):
-            result[mask] = np.nan
+            result[mask] = libmissing.NA
 
         if inplace:
             return self._update_inplace(result)
diff --git a/pandas/tests/extension/test_integer.py b/pandas/tests/extension/test_integer.py
index 936764c3627d0..65543cd6bbf1c 100644
--- a/pandas/tests/extension/test_integer.py
+++ b/pandas/tests/extension/test_integer.py
@@ -135,7 +135,7 @@ def _check_op(self, s, op, other, op_name, exc=NotImplementedError):
             expected = self._combine(s, other, op)
 
             if op_name in ("__rtruediv__", "__truediv__", "__div__"):
-                expected = expected.fillna(np.nan).astype("Float64")
+                expected = expected.fillna(pd.NA).astype("Float64")
             else:
                 # combine method result in 'biggest' (int64) dtype
                 expected = expected.astype(sdtype)
diff --git a/pandas/tests/series/methods/test_convert_dtypes.py b/pandas/tests/series/methods/test_convert_dtypes.py
index d91cd6a43daea..2d12ccab6f95c 100644
--- a/pandas/tests/series/methods/test_convert_dtypes.py
+++ b/pandas/tests/series/methods/test_convert_dtypes.py
@@ -193,7 +193,7 @@ def test_convert_dtypes(
         # Test that it is a copy
         copy = series.copy(deep=True)
 
-        result[result.notna()] = np.nan
+        result[result.notna()] = None
 
         # Make sure original not changed
         tm.assert_series_equal(series, copy)