Between 1913 and 1915, the original HRR line was realigned, and the station was rebuilt in order to accommodate both the Hudson Division of the New York Central Railroad and the connecting spur of the ND&C along the north side of Fishkill Creek.

Additionally, the station also contained a new ferry dock designed for trains, passengers, and eventually cars.

Amtrak took over intercity passenger service in 1971, but Beacon station continued to serve only Penn Central Hudson Line commuter trains which by that time ran to Poughkeepsie and was subsidized by the MTA beginning in 1972.

A fire in 1976 destroyed the station built by New York Central in 1913, which was demolished later that year to create more parking capacity.

[12][13] On October 17, 2005, ferry service to the station from Newburgh resumed after 42 years in which the Newburgh–Beacon Bridge had sufficed to bring people across the river.

On March 27, 2023, the Track 3 side platform opened for passenger service after a full reconstruction, and is accessible from the south end of the eastern parking lot, including via ADA-compliant ramps.