diff --git a/sklearn/manifold/_isomap.py b/sklearn/manifold/_isomap.py
index 914a012a0f0a0..e2451f31cc1c2 100644
--- a/sklearn/manifold/_isomap.py
+++ b/sklearn/manifold/_isomap.py
@@ -409,7 +409,13 @@ def transform(self, X):
 
         n_samples_fit = self.nbrs_.n_samples_fit_
         n_queries = distances.shape[0]
-        G_X = np.zeros((n_queries, n_samples_fit))
+
+        if hasattr(X, "dtype") and X.dtype == np.float32:
+            dtype = np.float32
+        else:
+            dtype = np.float64
+
+        G_X = np.zeros((n_queries, n_samples_fit), dtype)
         for i in range(n_queries):
             G_X[i] = np.min(self.dist_matrix_[indices[i]] + distances[i][:, None], 0)
 
diff --git a/sklearn/utils/estimator_checks.py b/sklearn/utils/estimator_checks.py
index 7026159f16287..7dc36ca8cd58e 100644
--- a/sklearn/utils/estimator_checks.py
+++ b/sklearn/utils/estimator_checks.py
@@ -1743,18 +1743,20 @@ def check_transformer_preserve_dtypes(name, transformer_orig):
         X_cast = X.astype(dtype)
         transformer = clone(transformer_orig)
         set_random_state(transformer)
-        X_trans = transformer.fit_transform(X_cast, y)
-
-        if isinstance(X_trans, tuple):
-            # cross-decompostion returns a tuple of (x_scores, y_scores)
-            # when given y with fit_transform; only check the first element
-            X_trans = X_trans[0]
-
-        # check that the output dtype is preserved
-        assert X_trans.dtype == dtype, (
-            f"Estimator transform dtype: {X_trans.dtype} - "
-            f"original/expected dtype: {dtype.__name__}"
-        )
+        X_trans1 = transformer.fit_transform(X_cast, y)
+        X_trans2 = transformer.fit(X_cast, y).transform(X_cast)
+
+        for Xt, method in zip([X_trans1, X_trans2], ["fit_transform", "transform"]):
+            if isinstance(Xt, tuple):
+                # cross-decompostion returns a tuple of (x_scores, y_scores)
+                # when given y with fit_transform; only check the first element
+                Xt = Xt[0]
+
+            # check that the output dtype is preserved
+            assert Xt.dtype == dtype, (
+                f"{name} (method={method}) does not preserve dtype. "
+                f"Original/Expected dtype={dtype.__name__}, got dtype={Xt.dtype}."
+            )
 
 
 @ignore_warnings(category=FutureWarning)