diff --git a/tests/functional/flakes/flakes.sh b/tests/functional/flakes/flakes.sh
index dfa088960..3ef518b23 100644
--- a/tests/functional/flakes/flakes.sh
+++ b/tests/functional/flakes/flakes.sh
@@ -485,6 +485,16 @@ nix flake lock $flake3Dir
 nix flake update flake2/flake1 --flake "$flake3Dir"
 [[ $(jq -r .nodes.flake1_2.locked.rev "$flake3Dir/flake.lock") =~ $hash2 ]]
 
+# Test updating multiple inputs.
+nix flake lock "$flake3Dir" --override-input flake1 flake1/master/$hash1
+nix flake lock "$flake3Dir" --override-input flake2/flake1 flake1/master/$hash1
+[[ $(jq -r .nodes.flake1.locked.rev "$flake3Dir/flake.lock") =~ $hash1 ]]
+[[ $(jq -r .nodes.flake1_2.locked.rev "$flake3Dir/flake.lock") =~ $hash1 ]]
+
+nix flake update flake1 flake2/flake1 --flake "$flake3Dir"
+[[ $(jq -r .nodes.flake1.locked.rev "$flake3Dir/flake.lock") =~ $hash2 ]]
+[[ $(jq -r .nodes.flake1_2.locked.rev "$flake3Dir/flake.lock") =~ $hash2 ]]
+
 # Test 'nix flake metadata --json'.
 nix flake metadata $flake3Dir --json | jq .