diff --git a/lib/tool_shed/webapp/model/__init__.py b/lib/tool_shed/webapp/model/__init__.py
index a0b1a178cdd5..445427d65c63 100644
--- a/lib/tool_shed/webapp/model/__init__.py
+++ b/lib/tool_shed/webapp/model/__init__.py
@@ -97,7 +97,7 @@ class APIKeys(Base):
     user_id: Mapped[Optional[int]] = mapped_column(ForeignKey("galaxy_user.id"), index=True)
     key: Mapped[Optional[str]] = mapped_column(TrimmedString(32), index=True, unique=True)
     user = relationship("User", back_populates="api_keys")
-    deleted: Mapped[Optional[bool]] = mapped_column(Boolean, index=True, default=False)
+    deleted: Mapped[Optional[bool]] = mapped_column(index=True, default=False, nullable=False)
 
 
 class User(Base, Dictifiable):
diff --git a/lib/tool_shed/webapp/model/migrations/alembic/versions/1b5bf427db25_add_non_nullable_column_deleted_to_api_.py b/lib/tool_shed/webapp/model/migrations/alembic/versions/1b5bf427db25_add_non_nullable_column_deleted_to_api_.py
new file mode 100644
index 000000000000..390402f37b53
--- /dev/null
+++ b/lib/tool_shed/webapp/model/migrations/alembic/versions/1b5bf427db25_add_non_nullable_column_deleted_to_api_.py
@@ -0,0 +1,61 @@
+"""add non-nullable column deleted to API keys
+
+Revision ID: 1b5bf427db25
+Revises: 969bbf7bcc29
+Create Date: 2024-05-29 21:53:53.516506
+
+"""
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy import (
+    Boolean,
+    Column,
+    false,
+    ForeignKey,
+    func,
+    Integer,
+    select,
+)
+
+from galaxy.model.database_object_names import build_index_name
+from galaxy.model.migrations.util import (
+    add_column,
+    drop_column,
+    drop_index,
+    transaction,
+)
+
+# revision identifiers, used by Alembic.
+revision = "1b5bf427db25"
+down_revision = "969bbf7bcc29"
+branch_labels = None
+depends_on = None
+
+# database object names used in this revision
+table_name = "api_keys"
+column_name = "deleted"
+index_name = build_index_name(table_name, column_name)
+
+
+def upgrade():
+    with transaction():
+        # Add a deleted column
+        add_column(table_name, Column(column_name, Boolean(), nullable=False, index=True, server_default=false()))
+        table = sa.sql.table(
+            table_name,
+            Column("id", Integer, primary_key=True),
+            Column("user_id", ForeignKey("galaxy_user.id"), index=True),
+            Column(column_name, Boolean, index=True, default=False),
+        )
+        # Set everything to deleted
+        op.execute(table.update().values(deleted=True))
+        # Select the latest api keys
+        s = select(func.max(table.c.id)).group_by(table.c.user_id)
+        # Set all of these api keys to not deleted
+        op.execute(table.update().where(table.c.id.in_(s)).values(deleted=False))
+
+
+def downgrade():
+    with transaction():
+        drop_index(index_name, table_name)
+        drop_column(table_name, column_name)