diff --git a/backend/pyproject.toml b/backend/pyproject.toml
index 0242be28..ef836a12 100644
--- a/backend/pyproject.toml
+++ b/backend/pyproject.toml
@@ -40,6 +40,13 @@ dev = [
 [tool.uv]
 package = true
 
+# Tell setuptools which directory IS the Python package.
+# Without this, having both `app/`, `alembic/`, `db/` at top level confuses
+# auto-discovery: "Multiple top-level packages discovered in a flat-layout".
+# We only want to package `app/`. `alembic/` and `db/` are operational, not Python packages.
+[tool.setuptools.packages.find]
+include = ["app*"]
+
 [tool.ruff]
 target-version = "py312"
 line-length = 100