| Name | | Location | Routes served |
| Albany Street Garage | | Albany Street, South End, Boston | Local, Mass Pike Express, and crosstown routes |
| Arborway Yard | | Washington Street, Jamaica Plain, Boston | Local bus routes; former terminus of the Green Line E branch |
| Cabot Garage | | Dorchester Avenue, South Boston | Local bus routes |
| Charlestown Garage | | Arlington Avenue, Charlestown, Boston | Local bus routes |
| Everett Shops | | Broadway, Everett | Heavy repair for buses and for subway components; former Orange Line terminus and yard |
| Fellsway Garage | | Salem Street, Medford | Local bus routes |
| Lynn Garage | | Western Avenue, Lynn | Local bus routes; North Shore express routes |
| North Cambridge Carhouse | | Massachusetts Avenue, North Cambridge | Formerly storage and maintenance for Harvard-based trolleybus routes; being converted for battery buses |
| Quincy Garage | | Hancock Street, Quincy | Quincy-based local bus routes |
| Somerville Garage at Charlestown | | Arlington Avenue, Charlestown, Boston | Local bus routes |
| Southampton Bus Maintenance Facility | | Southampton Street, South Bay, Boston | Silver Line dual mode buses; local bus routes |
| Watertown Yard | | Galen Street, Watertown | Midday layover for local bus routes; former terminus of the Green Line A branch and Green Line heavy maintenance facility |
| Name | | Location | Route | Use |
| Bradford Layover | | at | Haverhill Line | layover/storage |
| Franklin Layover | | east of | Franklin/Foxboro Line | layover/storage |
| Greenbush Layover | | at | Greenbush Line | layover/storage |
| Kingston Layover | | at | Kingston Line | layover/storage |
| MBTA Commuter Rail Maintenance Facility | | Inner Belt, Somerville | northside lines | Heavy maintenance for all commuter rail equipment; layover/storage |
| Middleboro Layover | | at | Fall River/New Bedford Line | layover/storage |
| Needham Layover | | south of | Needham Line | layover/storage |
| Newburyport Layover | | south of | Newburyport/Rockport Line | layover/storage |
| Pawtucket Layover | | Pawtucket, Rhode Island | Providence/Stoughton Line | layover/storage |
| Readville Interim Repair Facility | | north of | southside lines | Running maintenance and layover/storage. Expansion into a southside maintenance facility is planned. |
| Rochester Maintenance Facility | | Cape Main Line in Rochester | | Overhaul and maintenance |
| Rockport Layover | | at | Newburyport/Rockport Line | layover/storage |
| Southampton Street Yard | | south of South Station, Boston | southside lines | running maintenance and midday storage – primarily an Amtrak heavy maintenance facility |
| Stoughton Layover | | at | Providence/Stoughton Line | layover |
| Wamsutta Layover | | North of | Fall River/New Bedford Line | layover/storage |
| Weaver's Cove Layover | | North of | Fall River/New Bedford Line | layover/storage |
| West Cambridge Maintenance Facility | | south of | northside lines | Maintenance of way equipment storage |
| Westminster Layover | | west of | Fitchburg Line | layover/storage |
| Worcester Layover | | east of | Framingham/Worcester Line | layover/storage |
| Name | | Location | Routes | Use | Closed & reason |
| Attleboro Layover | | south of | Providence/Stoughton Line | layover/storage | 2006; replaced by Pawtucket Layover |
| Bennett Carhouse | | south of Harvard Square, Cambridge | Harvard-based streetcar and trackless trolley routes | maintenance and storage | 1970; Eliot Shops closed |
| Eliot Shops | | south of Harvard Square, Cambridge | Red Line | maintenance and storage | 1970; redevelopment |
| Fitchburg Layover | | east of | Fitchburg Line | layover/storage | 2016; replaced by [|Wachusett Layover] |
| Forest Hills Shops | | south of | Orange Line | maintenance and storage | 1987; completion of the southwest Corridor |
| Haverhill Layover | | north of | Haverhill Line | layover/storage | 1987; replaced by Bradford Layover |
| Ipswich Layover | | south of | Newburyport/Rockport Line | layover/storage | 1998; extension to Newburyport |
| Lechmere Yard | | at | Green Line | layover/storage | 2020; relocation of Lechmere station |
| Sullivan Square Shops | | at | Orange Line and streetcars | maintenance and storage | 1975; completion of the Haymarket North Extension |
| Bartlett Yard | | Roxbury near | MBTA bus and streetcars | maintenance and storage | 2005; operations moved to Arborway Yard in 2003 |