In addition to servicing some of the largest steamships of the era, the company maintained many of the yachts of New York's elite business community, and also occasionally built small watercraft such as tugboats.

Bethlehem Shipbuilding continued to utilize the yard as a ship conversion and repair facility until 1963, when it was closed due to declining profitability.

Five years later in 1885, he opened his own ship repair business, operated from a 25 × 40 ft (7.6 × 12.2 m) building at the foot of 26th Street, Brooklyn, which he named the Morse Iron Works.

[2] Customers by this time consisted not only of American and foreign shipping lines seeking repairs and maintenance for their vessels, but also New York's elite yachting community, which included some of America's wealthiest business tycoons.

[6] A month after the January 1900 incorporation, the Morse Works purchased the former property of the Atlantic Yacht Club between 55th and 57th Streets, Brooklyn, for the sum of $300,000, at the same time announcing the company's intention of shifting its locus of operations there, where it planned to build a sectional floating dry dock "capable of taking the largest ship afloat".

[7] In April, a large number of yachts moored at the site were given notice to move in order for construction of the dry dock to begin, and about twenty were subsequently relocated to Morse's existing plant at 26th Street.

In January 1903, the company asked for an extension of its loans due to tardy payments from the U.S. government, for whom it had recently completed a considerable amount of work.

However, in the same year, many of New York's shipbuilding and repair yards were hit by a series of labor strikes led by the International Association of Machinists, and the Morse Works was one of the worst affected.

[11] A few months later, in December 1905, an old wooden sidewheel steamer of the Joy Line called Rosalie, which had recently been laid up in Winter quarters at the Morse Works, caught fire, threatening several other ships at the yard, including the Army transport USAT McClellan and the City of Key West.

Eight ships docked at the works, some of which had been seized from Germany, and which were in the process of being refitted for U.S. government service, were safely towed into the bay while the fire was brought under control.

[14] To move materials around the yard, the company had its own dedicated "dry land transportation fleet" consisting of 28 trucks with capacities of between one and five tons, including three all-electric vehicles.

[20] By March 1919, the first three sections were ready and were put to use for the first time in lifting the steamer Black Arrow out of the water, at the rate of one foot per minute.

The company had its own simple health insurance scheme into which each employee paid 20 cents a week, which entitled him to pay of one dollar a day when sick, and $100 to his family in the event of his death.

During the war, many shipyards began publishing their own in-house newsletters which were distributed to their employees as a means of boosting workforce morale and productivity and increasing loyalty.

After the war, the number of these house organs grew dramatically, as they were also considered an important means of countering postwar, radical labor propaganda disseminated by the Industrial Workers of the World.

[33] The Morse company's own contribution to this field was The Dry Dock Dial, a 16-page periodical that was mailed out to employees' homes once a month.

Initially founded, in the words of E. P. Morse himself, "to bring our men closer together, to make them familiar with the doings in the yard and to arouse their interest in the welfare of the company",[34] the Dial was run by a professional staff of ex-newspapermen[35] and quickly established itself as the shipbuilding industry's leading in-house publication.

The magazine also catered to employees' spouses, with a women's page featuring baby pictures, recipes and other items deemed of interest to females.

The design, which featured a Morse company worker swinging a large sledgehammer toward a nest of threatening bayonets,[33] was later reproduced (without the accompanying caption) on the cover of the Dial's February 1919 edition.

The rebuilt Powhatan, renamed Cuba, underwent trials and began operation in late 1920 as the world's first passenger ship with an electric drive.

[41] In January 1921, an explosion on board the Standard Oil tanker Ardmore, under repair at the Morse yard, killed four men and injured several others.

[46][47] Having overseen the creation of United Dry Docks, Morse briefly served as chairman of the board before retiring from active business a few months later, returning to his native Nova Scotia where he died in August 1930 at the age of 72.