City commuters were warned Monday to prepare for “substantial” service cuts — including on Metro-North, the LIRR and subways — as Winter Storm Stella hits.

MTA officials are keeping a close eye on the storm and will close down lines as needed, Gov. Andrew Cuomo said.

Even before the storm starts, the agency plans to cut local, limited and express bus service by 30 percent.

The MTA plans to have 13,000 workers on duty to clear snow from tracks, trains and storage yards.

The agency promised to keep riders updated through its website and text and email alerts.