diff --git a/scvi/external/solo/_model.py b/scvi/external/solo/_model.py
index 779eecdd9b..0017a6fa18 100644
--- a/scvi/external/solo/_model.py
+++ b/scvi/external/solo/_model.py
@@ -235,6 +235,15 @@ def create_doublets(
             "sim_doublet_{}".format(i) for i in range(num_doublets)
         ]
 
+        # if adata setup with a layer, need to add layer to doublets adata
+        data_registry = adata.uns["_scvi"]["data_registry"]
+        x_loc = data_registry[_CONSTANTS.X_KEY]["attr_name"]
+        layer = (
+            data_registry[_CONSTANTS.X_KEY]["attr_key"] if x_loc == "layers" else None
+        )
+        if layer is not None:
+            doublets_ad.layers[layer] = doublets
+
         return doublets_ad
 
     def train(
diff --git a/tests/external/test_solo.py b/tests/external/test_solo.py
index cf1955e7da..121b005b04 100644
--- a/tests/external/test_solo.py
+++ b/tests/external/test_solo.py
@@ -25,7 +25,8 @@ def test_solo(save_path):
 def test_solo_multiple_batch(save_path):
     n_latent = 5
     adata = synthetic_iid()
-    setup_anndata(adata, batch_key="batch")
+    adata.layers["my_layer"] = adata.X.copy()
+    setup_anndata(adata, layer="my_layer", batch_key="batch")
     model = SCVI(adata, n_latent=n_latent)
     model.train(1, check_val_every_n_epoch=1, train_size=0.5)