diff --git a/doc/source/whatsnew/v1.4.0.rst b/doc/source/whatsnew/v1.4.0.rst
index 9d788ffcfabe1..b7df9aa692655 100644
--- a/doc/source/whatsnew/v1.4.0.rst
+++ b/doc/source/whatsnew/v1.4.0.rst
@@ -545,6 +545,7 @@ Other Deprecations
 - A deprecation warning is now shown for :meth:`DataFrame.to_latex` indicating the arguments signature may change and emulate more the arguments to :meth:`.Styler.to_latex` in future versions (:issue:`44411`)
 - Deprecated :meth:`Categorical.replace`, use :meth:`Series.replace` instead (:issue:`44929`)
 - Deprecated :meth:`Index.__getitem__` with a bool key; use ``index.values[key]`` to get the old behavior (:issue:`44051`)
+- Deprecated downcasting column-by-column in :meth:`DataFrame.where` with integer-dtypes (:issue:`44597`)
 -
 
 .. ---------------------------------------------------------------------------
diff --git a/pandas/core/internals/blocks.py b/pandas/core/internals/blocks.py
index 91c4946b64fe8..d9fc1a903009e 100644
--- a/pandas/core/internals/blocks.py
+++ b/pandas/core/internals/blocks.py
@@ -1227,6 +1227,15 @@ def where(self, other, cond) -> list[Block]:
             if m.any():
                 taken = result.take(m.nonzero()[0], axis=axis)
                 r = maybe_downcast_numeric(taken, self.dtype)
+                if r.dtype != taken.dtype:
+                    warnings.warn(
+                        "Downcasting integer-dtype results in .where is "
+                        "deprecated and will change in a future version. "
+                        "To retain the old behavior, explicitly cast the results "
+                        "to the desired dtype.",
+                        FutureWarning,
+                        stacklevel=find_stack_level(),
+                    )
                 nb = self.make_block(r.T, placement=self._mgr_locs[m])
                 result_blocks.append(nb)
 
diff --git a/pandas/tests/frame/indexing/test_where.py b/pandas/tests/frame/indexing/test_where.py
index 6ab0e2f718f8a..3d55ff5f98407 100644
--- a/pandas/tests/frame/indexing/test_where.py
+++ b/pandas/tests/frame/indexing/test_where.py
@@ -98,7 +98,7 @@ def test_where_upcasting(self):
 
         tm.assert_series_equal(result, expected)
 
-    def test_where_alignment(self, where_frame, float_string_frame):
+    def test_where_alignment(self, where_frame, float_string_frame, mixed_int_frame):
         # aligning
         def _check_align(df, cond, other, check_dtypes=True):
             rs = df.where(cond, other)
@@ -141,7 +141,11 @@ def _check_align(df, cond, other, check_dtypes=True):
 
         # check other is ndarray
         cond = df > 0
-        _check_align(df, cond, (_safe_add(df).values))
+        warn = None
+        if df is mixed_int_frame:
+            warn = FutureWarning
+        with tm.assert_produces_warning(warn, match="Downcasting integer-dtype"):
+            _check_align(df, cond, (_safe_add(df).values))
 
         # integers are upcast, so don't check the dtypes
         cond = df > 0
@@ -461,7 +465,7 @@ def test_where_complex(self):
         df[df.abs() >= 5] = np.nan
         tm.assert_frame_equal(df, expected)
 
-    def test_where_axis(self):
+    def test_where_axis(self, using_array_manager):
         # GH 9736
         df = DataFrame(np.random.randn(2, 2))
         mask = DataFrame([[False, False], [False, False]])
@@ -499,8 +503,10 @@ def test_where_axis(self):
         assert return_value is None
         tm.assert_frame_equal(result, expected)
 
+        warn = FutureWarning if using_array_manager else None
         expected = DataFrame([[0, np.nan], [0, np.nan]])
-        result = df.where(mask, s, axis="columns")
+        with tm.assert_produces_warning(warn, match="Downcasting integer-dtype"):
+            result = df.where(mask, s, axis="columns")
         tm.assert_frame_equal(result, expected)
 
         expected = DataFrame(
@@ -717,6 +723,23 @@ def test_where_try_cast_deprecated(frame_or_series):
         obj.where(mask, -1, try_cast=False)
 
 
+def test_where_int_downcasting_deprecated(using_array_manager):
+    # GH#44597
+    arr = np.arange(6).astype(np.int16).reshape(3, 2)
+    df = DataFrame(arr)
+
+    mask = np.zeros(arr.shape, dtype=bool)
+    mask[:, 0] = True
+
+    msg = "Downcasting integer-dtype"
+    warn = FutureWarning if not using_array_manager else None
+    with tm.assert_produces_warning(warn, match=msg):
+        res = df.where(mask, 2 ** 17)
+
+    expected = DataFrame({0: arr[:, 0], 1: np.array([2 ** 17] * 3, dtype=np.int32)})
+    tm.assert_frame_equal(res, expected)
+
+
 def test_where_copies_with_noop(frame_or_series):
     # GH-39595
     result = frame_or_series([1, 2, 3, 4])
diff --git a/pandas/tests/frame/methods/test_clip.py b/pandas/tests/frame/methods/test_clip.py
index c851e65a7ad4f..e692948c92a26 100644
--- a/pandas/tests/frame/methods/test_clip.py
+++ b/pandas/tests/frame/methods/test_clip.py
@@ -136,7 +136,7 @@ def test_clip_against_unordered_columns(self):
         tm.assert_frame_equal(result_lower, expected_lower)
         tm.assert_frame_equal(result_lower_upper, expected_lower_upper)
 
-    def test_clip_with_na_args(self, float_frame):
+    def test_clip_with_na_args(self, float_frame, using_array_manager):
         """Should process np.nan argument as None"""
         # GH#17276
         tm.assert_frame_equal(float_frame.clip(np.nan), float_frame)
@@ -151,7 +151,9 @@ def test_clip_with_na_args(self, float_frame):
         )
         tm.assert_frame_equal(result, expected)
 
-        result = df.clip(lower=[4, 5, np.nan], axis=1)
+        warn = FutureWarning if using_array_manager else None
+        with tm.assert_produces_warning(warn, match="Downcasting integer-dtype"):
+            result = df.clip(lower=[4, 5, np.nan], axis=1)
         expected = DataFrame(
             {"col_0": [4, 4, 4], "col_1": [5, 5, 6], "col_2": [7, 8, 9]}
         )