Jabarkan Combined operations dari MBTA Commuter Rail

Rapid transit extension was slower than expected; by 1971, the only extension in service was the first portion of the Red Line Braintree Branch on the Old Colony mainline. In 1972, as part of a funding shift from highways to transit, Governor Francis Sargent initiated a Commuter Rail Improvement Program. On October 8, 1974, the MBTA began using purple to represent the commuter rail system, as had been done in 1965 with the rapid transit lines. MBTA maps began showing the B&M and Penn Central lines as a single system. Penn Central became Conrail on April 1, 1976; the MBTA purchased most of their commuter rolling stock at that time. After delays due to the B&M bankruptcy, the MBTA purchased the B&M commuter equipment, maintenance facility, and  of right of way on December 27, 1976. This included all lines with passenger service, as well as a number of freight-only or abandoned lines. This also marked the start of a five-year contract for the B&M to operate the service, replacing a series of one-year contracts. 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.

Federal subsidies allowed MBTA subsidies to Penn Central to remain the same until March 1977, when a large increase was expected. Since it owned the tracks and equipment, the MBTA bid out the operating contract, which was won by the B&M.  The B&M began operating the southside lines on March 15, 1977; for the first time, all Boston commuter service was operated by one entity. Although all operation was subsidized by this time, a small number of cuts took place. The lightly used Lexington Branch closed after a snowstorm on January 10, 1977. Declining subsidies from Rhode Island resulted in off-peak  service being cut back to  in April 1979, with peak service cut on February 20, 1981. Woburn Branch service ended on January 30, 1981, amid state budget cuts.

However, the energy crises of the 1970s and the formation of regional transit authorities prompted some expansions and improvements. $70 million in reconstruction work (equivalent to  million in ) on the Franklin Line and several northside lines, partially funded by the Urban Mass Transportation Administration, began in 1977 under the Commuter Rail Improvement Program. Service to Haverhill resumed on December 17, 1979, and to  and  on January 13, 1980. Federally-funded experimental service to Nashua, Manchester, and Concord, New Hampshire ran from January 28, 1980, to March 1, 1981. Little-used stations continued to be closed until the 1980s, but several infill stations were opened, including  in 1981,  in 1982,  in 1984, and  in 1985. The MBTA also began replacing the aging Rail Diesel Cars and other equipment; 18 EMD F40PH diesel locomotives and 60 passenger cars arrived between 1978 and 1980.

Several major disruptions occurred in the mid-1980s. On January 20, 1984, a fire destroyed the wooden approach trestles to the North Station drawbridges. The four northside lines used temporary terminals with rapid transit connections while the trestles were rebuilt. Another bridge fire between Beverly and Salem on November 16, 1984, isolated part of the Ipswich/Rockport Line from the rest of the system. Service to North Station resumed on April 20, 1985; service to Ipswich and Rockport resumed on December 1, 1985.

Guilford Transportation Industries purchased the B&M in 1983. This did not initially affect commuter rail operations. Guilford's attempts to regain profitability, which included reducing employee headcount and pay, soon soured labor relations. This resulted in two strikes by Guilford employees; the first shut down the commuter rail system from March 21 to May 12, 1986. 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. Amtrak won the contract for commuter rail operations and took over the system on January 1, 1987. Gardner service was cut back to Fitchburg at that time due to a dispute between Amtrak, Guilford, and the MBTA.