He began his business career in Scarborough, Maine where he had a store on the Dunstan Landing Road. He was an owner of lands in Rowley-Canada which had been granted to soldiers who had served in the Canada Expedition and the Siege of Fort Nashwaak which he lost in a boundary line dispute between Massachusetts and New Hampshire. As a result of losing these lands he and 2 others were granted, in 1761, a township named Pondicherry, now Bridgton, Maine, seven miles square, east of the Saco River. He was one of three who proceeded to lay out the township and received the land grant for the entire township on June 25, 1765. Finding the timber on these lands too remote from a market Milliken sold out his share and invested in lands adjoining other lands owned by him on the Union River that he bought in 1769 from William Maxfield He had business reversals, lost his lands and other property in Scarborough, Maine and in 1764 made Trenton, Maine his headquarters. He was granted a mill privilege there with timber lands adjoining. He and his brother Thomas Milliken built a dam and mill on the Union River at or near the head of the tide, close to where the Bangor Hydro Dam exists. It may have been tidal powered but proved a failure was called the " Folly Mill," and was soon abandoned. Afterwards the Benjamin and Thomas Milliken built a double saw-mill, at the Head Tide Dam on the Union River at what became the Union River Settlement of which City Benjamin Milliken is acknowledged the founder. When the second dam was built by the Millikens, they were either unable to build the whole or sold the rights to the western bank, and the settlers on the west side of the Union River, John Murch and Benjamin Joy built a mill. The Ellsworth hydro-electric dam begun in 1907 is located at the site of one of the original Benjamin Milliken Union River dams. Milliken also owned vessels, and shipped lumber to Connecticut. In 1773 the first schooner built at Ellsworth, Maine, on the Union River was named the "Susan and Abigail", after the daughters of its two most prominent citizens, Benjamin Milliken and Benjamin Joy. The vessel carried pine shingles and oak staves in annual voyages to the West Indies. This trade was the township's primary business for some time. A British cruiser destroyed the "Susan and Abigail" during the American War of Independence.
American rebels called Milliken "Royalist Ben", "Tory Ben" and "Runaway Ben" as he expressed Tory sentiments when the American War of Independence broke out and was a loyal supporter of King George III. He first joined the British at Bagaduce, on Penobscot Bay after his home, grist & saw mills and farm, were destroyed by rebel forces. During the early years of the American War of Independence he served as a pilot on British Ships and transported lumber and supplies to a British garrison under the command of a General Francis McLean at Fort Majebigwaduce . He was taken prisoner at Castine in July 1779 by rebel Colonel John Allan and a band of Native Americans who put him in irons. He was imprisoned on board the rebel frigate part of the fleet that commenced the Siege of Penobscot. British troops constructed Fort George while fighting the American rebels for three weeks, during which time Benjamin Milliken was held prisoner. During the Siege Milliken's house was plundered by American rebels. A group of rebels led by an officer entered the house and attempted to force their way into Milliken's wife Phebe's bedroom where the silver plate and other valuables were concealed. One of the Milliken's female domestics placed her hand upon the latch of the door, the officer drew his sword and nearly severed her fingers, she stood firm holding up her dripping hand before her face, saying, "There, sir, is better blood than runs in your veins". The rebels ransacked the house and then drove the cattle belonging to the Milliken estate into the kitchen and slaughtered them, leaving the offal in the floor. On the twenty-first day of the Penobscot Siege, on August 14, 1779, three British frigates of war commanded by Sir George Collier arrived. The American fleet unable to escape ran their boats ashore up the Penobscot River, released their prisoners including Benjamin Milliken, set fire to their fleet and escaped by foot into the woods. It was the greatest loss in American Naval history until Pearl Harbour.
Later years
He moved to New Brunswick in 1782-3. On Aug. 12, 1784, he, with about one hundred others, known as the Penobscot Association Loyalists, received two grants of land from the British Crown. Their town grant comprised the town plot of St. Andrew's New Brunswick and their farm lots under separate grants included several tracts extending from Bocabec westerly along the coast to St. Stephen, with an additional tract on the St. Croix River above what is now St. Stephen, New Brunswick. Shortly after these lands were granted Milliken left St. Andrew's and moved to Bocabec, New Brunswickon the shore of Passamaquoddy Bay near St. Andrew's where he built a shipyard and lived out the remainder of his life. He was a pioneer settler three times in British North America starting in Scarborough, Maine, then on the Union River as the founder of Ellsworth, Maine and then in St. Andrew's and Bocabec, New Brunswick.