Jabarkan Consolidation under MBTA control dari MBTA Commuter Rail

The three railroads all made major cuts to suburban service in 1958–1960 as commuters began using new expressways. The B&M became unprofitable in 1958 and moved to shed its money-losing passenger operations. Four branch lines were cut that May, and most stations in the MTA service area were closed; three more branches closed in 1959. The New Haven experimentally increased Old Colony Division service for several years in the 1950s, but new management soon sought to reduce costs. Service to  and  was cut in 1958; a one-year state subsidy was given for the remaining Old Colony service, which ended in 1959 after the Southeast Expressway opened. The inner portion of the B&A was reduced from four to two tracks in 1959 for construction of the Massachusetts Turnpike, with several inner stations closed; all local stops west of Framingham were closed in 1960. The New Haven filed for bankruptcy for the last time in 1961. Faced with the imminent threat of losing what service remained, public opinion began to support subsidies for commuter rail.

The state Mass Transportation Commission (MTC), formed in 1959 to coordinate transportation and land use, held a series of experiments to determine how fares and service levels affected ridership. This included a trial on the MTA bus network, as well as a $4 million test from January 1963 to March 1964 on New Haven and B&M lines. (The NYC, uninterested in its commuter service, declined to participate.) The MTC found that higher frequency was most important to attract additional ridership; lower fares would attract additional riders, while even higher fares would not result in the services becoming profitable. At the recommendation of the MTC, the Massachusetts Bay Transportation Authority (MBTA) was created on August 3, 1964, with a 78-municipality funding and service district. The MBTA was to build rapid transit extensions (as planned in 1947) along some lines, with the others to be subsidized or allowed to be discontinued. Most remaining lines ran to points outside the funding district; those outlying municipalities were expected to reach their own subsidy agreements with the railroads.

On December 14, 1964, the MBTA reached a subsidy agreement with the B&M. The agreement only covered in-district services; on January 5, 1965, the B&M discontinued interstate service except for single commuter round trips from Dover and Concord, New Hampshire; Portsmouth service was cut back to a single  round trip. Subsidies began for six lines on January 18; all out-of-district service to , , , , and  was discontinued except for three single round trips. Agreements were reached to restore most out-of-district service; after delays due to a lawsuit by the competing Eastern Massachusetts Street Railway, full service returned to , Lowell, Ipswich, and Rockport on June 28. On June 30, 1967, the B&M discontinued the Concord trip; the Dover trip was cut back to Haverhill with local subsidies. In 1969, the B&M averaged 24,000 weekday passengers, with a yearly deficit of $3.2 million (equivalent to  million in ). The single daily trip on the Central Mass Branch ended on January 26, 1971.

On July 28, 1965, the MBTA signed an agreement with the New Haven Railroad to purchase  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. The line was expected to be completed within two years. The agreement also provided for the MBTA to subsidize commuter service on the railroad's remaining commuter rail lines for $1.2 million (equivalent to  million in ) annually. 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. Three out-of-district stations were cut, while Franklin subsidized its station. The Millis and Dedham lines were discontinued on April 21, 1967. The NYC and the Pennsylvania Railroad merged to form Penn Central on February 1, 1968; the New Haven joined at the end of the year. Penn Central declared bankruptcy in 1970. Amtrak took over most intercity passenger service in the US on May 1, 1971, including New York–Boston trains.

The state agreed in December 1971 to purchase  of Penn Central rights of way to prevent them being sold off in bankruptcy. The MBTA purchased the lines effective January 27, 1973. They included almost all the lines with passenger service: the Attleboro Line and Stoughton Branch, Franklin Branch, Needham Branch, and the –Framingham portion of the Worcester Main Line. (The inner section of that line was already owned by the Massachusetts Turnpike Authority.) The purchase also included several freight-only or abandoned lines, including the Old Colony mainline between Braintree and Brockton. Subsidies began for the Framingham Line in January 1973, for  and  stations in June 1973, and all Providence/Stoughton Line service on September 28, 1976. The MBTA purchased the B&M Western Route between Somerville and Wilmington Junction in September 1973 for construction of the Haymarket North Extension

From 1967 to 1973, a series of state appropriations covered 90–100% of outside-of-district subsidy. This was reduced to 50% in January 1974, substantially increasing the cost of these municipalities. This resulted in several cuts as municipalities refused the higher subsidies: Ayer service was cut to  on March 1, 1975; the single Newburyport trip ended on April 1, 1976; and the single Haverhill trip ended on April 2, 1976 (North Andover and Andover having previously ended subsidies.) The single round trip to , never subsidized, was cut to Framingham on October 27, 1975. Amtrak began running the Lake Shore Limited over that route four days later, restoring rail service to Worcester. State subsidies were increased back to 75% in June 1976 to prevent further cuts.