Abbott was born in St. Andrews, Lower Canada (now Saint-André-d'Argenteuil, Quebec), to Harriet (née Bradford) and the Rev. Joseph Abbott (an Anglican missionary). In 1849, Abbott married Mary Martha Bethune (1823–1898), a relative of Dr. Norman Bethune, a daughter of Anglican clergyman and McGill acting president John Bethune, and a granddaughter of the Presbyterian minister John Bethune. The couple had four sons and four daughters, many of whom died without descendants. Their eldest surviving son, William Abbott, married the daughter of Colonel John Hamilton Gray, a Father of Confederation and Premier of Prince Edward Island. The direct descendants of Abbott and Hamilton Gray include John Kimble Hamilton ("Kim") Abbott, a political commentator and lobbyist and a WWII Royal Canadian Airforce pilot in the infamous "Demon Squadron". Abbott was also the great-grandfather of Canadian actor Christopher Plummer and the first cousin (once removed) of Maude Abbott, one of Canada's earliest female medical graduates and an expert on congenital heart disease.
In 1849, he signed the Montreal Annexation Manifesto calling for Canada to join the United States, an action which he regretted later as a youthful error. He eventually joined the Loyal Orange Lodge of British North America, well known as a pro-British organization. Abbott first ran for Canada's Legislative Assembly in 1857 in the Argenteuil district, northwest of Montreal. Defeated, he challenged the election results on the grounds of voting list irregularities and was eventually awarded the seat in 1860. He served as solicitor general for Lower Canada (Quebec) representing the conservative administration of John Macdonald and Louis Sicotte, from 1862 until 1863. He reluctantly supported Canada's confederation, fearing the reduction of the political power of Lower Canada's English-speaking minority. In 1865, he converted to a conservative. His proposal to protect the electoral borders of 12 English Quebec constituencies was eventually incorporated into the British North America Act 1867.