diff --git a/CHANGELOG.md b/CHANGELOG.md
index 85b0f336de..ff887cd417 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -98,6 +98,7 @@ to [Semantic Versioning]. Full commit history is available in the
 
 #### Fixed
 
+- Fix logging of accuracy for cases with 1 sample per class in scANVI {pr}`2938`.
 - Disable adversarial classifier if training with a single batch.
     Previously this raised a None error {pr}`2914`.
 - {meth}`~scvi.model.SCVI.get_normalized_expression` fixed for Poisson distribution and
diff --git a/src/scvi/train/_trainingplans.py b/src/scvi/train/_trainingplans.py
index 2f111e5dc1..b6eea8ab7e 100644
--- a/src/scvi/train/_trainingplans.py
+++ b/src/scvi/train/_trainingplans.py
@@ -741,7 +741,7 @@ def compute_and_log_metrics(
             return
 
         classification_loss = loss_output.classification_loss
-        true_labels = loss_output.true_labels.squeeze()
+        true_labels = loss_output.true_labels.squeeze(-1)
         logits = loss_output.logits
         predicted_labels = torch.argmax(logits, dim=-1)