Allen was forced to end his studies upon his father's death. He volunteered for militia service in 1757 in response to the French siege of Fort William Henry, but his unit received word that the fort had fallen while they were en route, and they turned back. The French and Indian War continued over the next several years, but Allen did not participate in any further military activities and is presumed to have tended his farm. In 1762, he became part owner of an iron furnace in Salisbury. He also married Mary Brownson from Roxbury in July 1762, who was five years his senior. They first settled in Cornwall, but moved the following year to Salisbury with their infant daughter Loraine. They bought a small farm and proceeded to develop the iron works. The expansion of the iron works was apparently costly to Allen; he was forced to sell off portions of the Cornwall property to raise funds, and eventually sold half of his interest in the works to his brother Heman. The Allen brothers sold their interest in the iron works in October 1765.