After leaving office, Abernethy continued doing well in his business. Among other things he served as the Oregon City agent for the pioneer steamer "Lot Whitcomb", the first steam-powered vessel built on the Willamette River and the second one built in the entire Oregon Country. Abernethy's assets were destroyed during the flood of 1861. He moved to Portland shortly after. He died in 1877 at 70 years of age. Abernethy was buried at River View Cemetery.