In 1881, BH&E successor New York and New England Railroad (NY&NE) began using the southwestern portion of the ND&C.

[1]: 14  It was to run from Plumb Point in Fishkill northeast to meet the New York and Harlem Railroad at Hillsdale station in Craryville.

[3]: 7  Columbia County townships proved reluctant to fund the northern portion of the line, so it was rerouted eastward from Pine Plains to meet the Harlem at Millerton.

[6] Intending to bypass New York City and compete with the New York, New Haven and Hartford Railroad (New Haven) for New England business, the Erie Railroad (which controlled the BH&E) planned to ship coal across the Hudson River from Newburgh.

In the early morning hours of March 22, the president and secretary led what a local historical society later called a "dramatic midnight train run".

[5]: 23  Beginning at Pine Plains, they tore up tracks at the engine house, woke up a conductor to operate a train, and took possession of the stations along the line.

[2]: 24 [5]: 23 [10] Regular service on the line resumed by March 25 using a purchased locomotive and coaches rented from the Hudson River Railroad.

[18][19] In 1873, it joined with the Harlem Extension and the unbuilt Pine Plains and Albany Railroad to form the New York, Boston and Montreal Railway (NYB&M).

[21] The Rhinebeck and Connecticut Railroad opened in 1875 with a shorter and flatter route to the Hudson than the D&C, which allowed it to charge lower rates.

[27][28] Train ferry service across the Hudson, connecting with the Erie Railroad, also began that day; the first freight car carried 800 turkeys from Livonia, New York, bound for Providence.

[29] Within weeks, the NY&NE was carrying more freight than all other railroads in Dutchess County combined.

[3]: 24  The Clove Branch, leased by the ND&C, ended service in 1897 as the iron mines ran out and was torn up in 1898.

[1]: 14 The CNE soon began to consolidate its duplicative lines crossing rural Dutchess County.

Trains were rerouted over the parallel ex-Poughkeepsie and Eastern, including the portion of the ex-ND&C between Pine Plains and Stissing Junction.

[42][43] That 7.73-mile (12.44 km) section of track was generally disused for freight until January 21, 1925, when the Interstate Commerce Commission authorized abandonment.

[45]: 6 [51] On July 1, 1936, the New Haven discontinued freight service between Stissing Junction and Millbrook because two trestles were in poor condition.

[45]: 11 [52] In April 1938, the Interstate Commerce Commission allowed the New Haven to abandon most of the remaining ex-CNE lines in New York.

The New Haven continued operating the Maybrook Line as a major freight route over the Poughkeepsie Bridge.

The Poughkeepsie Bridge was damaged by fire in 1974, cutting off the Maybrook Line from west-of-Hudson connections.

This left the ex-ND&C spur to Beacon as the only western connection for the line; Conrail soon upgraded it to handle additional freight traffic.

[54][55] However, in 1981, Conrail applied to abandon the segment along with the Maybrook Line between Poughkeepsie and Hopewell Junction (the former Dutchess County Railroad).

[58] In early 2023, Metro-North filed for federal permission to acquire the Housatonic's freight rights and to discontinue the New York portion of the Beacon Line, which would be converted to a rail trail.

[2]: 19  From there the line gradually turned northward into steeper terrain, with a difficult grade from Moore's Mills to Verbank then a curving route around Oak Summit into Millbrook.

[2]: 20 [3]: 11 The Poughkeepsie and Eastern Railway joined the ND&C at Stissing Junction, with trackage rights on the ND&C up to a split just south of Pine Plains.

Some 3.5 miles (5.6 km) of 1.5% downgrade followed as the line approached Millerton, where it crossed the New York and Harlem Railroad.

[67] The maximum speed allowed between State Line and Pine Plains for passenger trains was just 23 miles per hour (37 km/h) due to the steep grades.

[69]: 18 A short branch at the southwest end, originally constructed by the NY&NE, split at Wicopee Junction west of Matteawan.