diff --git a/src/scanpy/plotting/_tools/scatterplots.py b/src/scanpy/plotting/_tools/scatterplots.py
index 30356d8b04..840c13a3eb 100644
--- a/src/scanpy/plotting/_tools/scatterplots.py
+++ b/src/scanpy/plotting/_tools/scatterplots.py
@@ -294,9 +294,9 @@ def embedding(  # noqa: PLR0912, PLR0913, PLR0915
         elif sort_order and color_type == "cat":
             # Null points go on bottom
             order = np.argsort(~pd.isnull(color_source_vector), kind="stable")
-        # Set orders
-        if isinstance(size, np.ndarray):
-            size = np.array(size)[order]
+        # Set orders — use a local to avoid cumulative reordering across
+        # subplots when multiple color keys are given.
+        _size = np.array(size)[order] if isinstance(size, np.ndarray) else size
         color_source_vector = color_source_vector[order]
         color_vector = color_vector[order]
         coords = basis_values[:, dims][order, :]
@@ -348,10 +348,10 @@ def embedding(  # noqa: PLR0912, PLR0913, PLR0915
             )
         else:
             scatter = (
-                partial(ax.scatter, s=size, plotnonfinite=True)
+                partial(ax.scatter, s=_size, plotnonfinite=True)
                 if scale_factor is None
                 else partial(
-                    circles, s=size, ax=ax, scale_factor=scale_factor
+                    circles, s=_size, ax=ax, scale_factor=scale_factor
                 )  # size in circles is radius
             )
 
@@ -366,7 +366,7 @@ def embedding(  # noqa: PLR0912, PLR0913, PLR0915
                 # with some transparency.
 
                 bg_width, gap_width = outline_width
-                point = np.sqrt(size)
+                point = np.sqrt(_size)
                 gap_size = (point + (point * gap_width) * 2) ** 2
                 bg_size = (np.sqrt(gap_size) + (point * bg_width) * 2) ** 2
                 # the default black and white colors can be changes using