Five additional stations (Prides Crossing, Mishawum, Hastings, Plimptonville, and Plymouth) are indefinitely closed due to service cuts during the COVID-19 pandemic.

Special express service to Foxboro station is operated during New England Patriots home games and some other events at Gillette Stadium.

During the winter, one "ski train" round trip of the Fitchburg Line operates with a bicycle car on weekends and Wednesday evenings, with a shuttle bus to Wachusett Mountain.

The New Haven tested electrification on small parts of the Old Colony system, but never followed through on its plans to electrify South Station and the inner section of the ex-B&P.

Faced with the imminent threat of losing what service remained, public opinion began to support subsidies for commuter rail.

Most remaining lines ran to points outside the funding district; those outlying municipalities were expected to reach their own subsidy agreements with the railroads.

Subsidies began for six lines on January 18; all out-of-district service to Fitchburg, Lowell, Haverhill, Ipswich, and Rockport was discontinued except for three single round trips.

[30] On July 28, 1965, the MBTA signed an agreement with the New Haven Railroad to purchase 11 miles (18 km) of the former Old Colony mainline from Fort Point Channel to South Braintree in order to construct a new rapid transit line along the corridor.

[30][32] Subsidies for the Needham, Millis, Dedham, and Franklin lines began on April 24, 1966, as the New Haven had Interstate Commerce Commission (ICC) permission to discontinue them otherwise.

[30] In 1972, as part of a funding shift from highways to transit, Governor Francis Sargent initiated a Commuter Rail Improvement Program.

[30] After delays due to the B&M bankruptcy, the MBTA purchased the B&M commuter equipment, maintenance facility, and 250 miles (400 km) of right of way on December 27, 1976.

[30][28]: 16  After acquiring the B&M and Penn Central rolling stock, the MBTA painted it with purple, yellow, silver, and black to create a visual identity.

Local media was critical of Guilford during the strike; the company did not bid for a renewal of the commuter rail operating contract, which expired at the end of 1986.

[30][39] The Franklin Line was extended to Forge Park/495 in 1988; infill stations in that era included Yawkey in 1988 to serve Boston Red Sox games at Fenway Park, and Dedham Corporate Center in 1990.

[53] Free Wi-Fi internet service was piloted in January 2008 on the Worcester Line, where 45 coaches were fitted with routers which connected to cellular data networks.

[56][57] The MBTA canceled the plan in August 2017 due to local opposition to the erection of 320 monopoles, each 70-foot (21 m) tall, as well as the need to focus on more critical projects like the Green Line Extension.

[60][61] Positive Train Control was implemented on the entire system per a federal mandate, which required installation by the end of 2018 with the possibility of a two-year extension.

[73][74] That day, temporary reduced schedules were again put into place, with four of the five stations (Hastings, Silver Hill, Prides Crossing, and Plimptonville) not served.

[87] All MBTA commuter rail service is provided by push-pull trains powered by diesel locomotives with a cab car on the opposite end.

[90] A large midday and overnight layover yard, which would support expanded service including regional rail and electrification, is planned at Widett Circle near South Station.

[98] An $165 million option for 39 additional coaches (29 trailers and 10 cab cars), which would allow the retirement of all remaining single-level equipment, was exercised in November 2024 with deliveries to begin in 2027.

[104] The study's preferred alternative was a hybrid approach that combined elements of a urban rail concept (electrified rapid-transit frequencies within Greater Boston) and conventional regional rail options on longer lines, focusing on enhanced service on the busiest lines with the phased implementation of overhead electrification and electric multiple units.

By mid-2022, lawmakers and environmental advocacy groups had criticized recent MBTA proposals for not adhering to previously set rail initiatives.

[116] Early-action regional rail projects including designs for power systems, substations, signal upgrades, and track improvements along with the procurement of 25 EMUs are planned for fiscal years 2025 to 2029.

[118] Transit advocates have expressed concern that a battery-electric service plan remains unproven for regional rail applications and could be more expensive to operate than full-build electrification; others have criticized that the MBTA's cost and construction projections for system-wide catenary installation were overestimated in comparison to similar project costs in Europe and North America.

[119][120] In December 2023, Keolis solicited a proposal to procure BEMUs and implement 20-minute headways on the Fairmount Line by 2027 as leverage for contract renewal; the MBTA issued a notice of due diligence.

[122] The MBTA board approved the $54 million Fairmount Line proposal from Keolis in July 2024, with the new equipment to enter service in early 2028.

[126] By the mid-2020s, the MBTA had adapted short-term plans for regional rail to instead optimize diesel-hauled operations for increased services on select corridors, with electrification being implemented later after 2030 (with the exception of the Fairmount Line).

[128] In December 2024, the MBTA indicated plans to implement 30-minute all-day headways on the Framingham/Worcester Line by FY 2026; train consists would be shortened to 4 coaches long to enable higher frequencies.

[129] No direct connection exists between the two downtown commuter rail terminals; passengers must use the MBTA subway or other modes to transfer between the two halves of the system.