East of the Long Island City station, the abandoned Montauk Cutoff merges with the branch, after both cross Dutch Kills.

Soon after, full control of the Lower Montauk was transferred to the New York and Atlantic Railway for freight operations.

[6][7] The New York City Department of Transportation has periodically floated proposals to repurpose the Lower Montauk Branch for rapid transit operations.

The terminal stations in diesel territory, east of Babylon, are Patchogue, Speonk, Southampton, and Montauk; South Fork Commuter Connection shuttles may short-turn at Hampton Bays and Amagansett.

In the summer, with travelers going out to The Hamptons, Fire Island and other beaches, additional service is operated to the far eastern terminal at Montauk, such as the Cannonball, a Friday afternoon train departing from Penn Station (originally Hunterspoint Avenue) and running non-stop to Westhampton station in Westhampton.

In early times, the Scoot ran frequently between Greenport on the North Fork, "around the horn" on the Manorville Branch, and east to Sag Harbor.

This change resulted in the closure of the Southern's Berlin, Beaver Street (Jamaica), Locust Avenue, and Springfield stations.

[19] On July 27, 1881, after the South Side became part of the LIRR, its line – then the Montauk Division – was extended east to the Sag Harbor Branch at Eastport.

[17] The Montauk station was initially near the center of a sleepy fishing village at the north end of Fort Pond (where Austin Corbin built a pier in his unsuccessful effort to have trans-Atlantic ships dock there.)

In 1953, amid bankruptcy, the LIRR sought to abandon the Montauk branch east of Patchogue and operate bus service in its place.

It cited low, predominantly non-commuter ridership and proximity to the Main Line, and potential savings of $450,000 per year, equal to $5,288,619 today.

[28] The Town of East Hampton protested this proposed closure, highlighting the potential for increased vehicular traffic due to lack of alternative means of travel,[28] and the line ultimately remained open.

[29] Southampton College was temporarily reinstated for the 2004 and 2018 U.S. Open tournaments at the nearby Shinnecock Hills Golf Club, along with a steel walkway over Montauk Highway.

The funding would be used by the LIRR to design three passing sidings to be installed on the line in single-track territory between Speonk and Montauk.