Lachlan McIntosh was born near Raits, Badenoch, Scotland. After his father's death, McIntosh was sent to the Bethesda Orphanage in Savannah under the care of famous evangelist George Whitefield. He spent two years at the orphanage before traveling to Fort Frederica to serve as a military cadet. During this time, the Jacobite Rebellion broke out in Scotland. Lachlan and his brother William planned to travel to Scotland and join the rebellion, but General James Oglethorpe, who had become a friend and mentor to the young McIntosh, convinced them to remain in Georgia.

Lachlan's brother William has sometimes been confused with another William McIntosh of the Creek Nation, who is actually Lachlan and William McIntosh's cousin. The half Creek, half white leader William MacIntosh was the son of Capt. William MacIntosh, a Tory in the Rev. War., who was the son of Capt. John MacIntosh. This John MacIntosh, along with his brother Roderick, had come with John Mohr MacIntosh from Scotland. Confusion about the names stems from the fact that on the ship "The Prince of Wales" there had been at least five males named John MacIntosh in one form or another.

In 1748, McIntosh moved to Charleston, South Carolina, and took a position as a clerk for Henry Laurens, a wealthy merchant, who would become a lifelong friend and mentor. In 1756 he married Sarah Threadcraft. He soon returned to Georgia where he studied surveying and acquired land in the Altamaha River delta and became a prosperous rice planter.

By 1770, McIntosh had become a leader in the independence movement in Georgia. In January 1775 he helped organize delegates to the Provincial Congress from the Darien District of St. Andrew Parish. On January 7, 1776, McIntosh was commissioned as a colonel in the Georgia Militia. He raised the 1st Georgia Regiment of the Georgia Line, organized the defense of Savannah and helped repel a British assault at the Battle of the Rice Boats in the Savannah River. He was promoted to the rank of brigadier general in the Continental Army, charged with defense of Georgia's southern flank from British incursions from Florida, by then a British possession. On October 22, 1776, McIntosh ordered his brother William to construct a fort on the Satilla River to protect Georgia from Florida. The fort was the first to be named Fort McIntosh.

During the period of 1776 to 1777, McIntosh became embroiled in a bitter political dispute with Button Gwinnett, the Speaker of the Georgia Provisional Congress and a radical Whig leader. Their bitter personal rivalry began when McIntosh succeeded Gwinnett as commander of Georgia’s Continental Battalion in early 1776. The two men represented opposing factions is a deeply divided Patriot movement in Georgia. Gwinnett had been forced to step aside after his election had been called into question by opposing forces within the independence movement. Gwinnett, thwarted in his military ambitions, became a delegate to the Continental Congress and a signer of the United States Declaration of Independence. He returned to Georgia after his allies gained control of the Provisional Congress and succeeded in electing him speaker. Shortly afterward, he was elected president and commander-in-chief of the Committee of Safety.

Gwinnett began purging the government and military of his political rivals. One of the early targets of Gwinnett’s wrath was McIntosh’s brother George, who had opposed Gwinnett’s election. George was arrested and charged with treason against the revolution. In addition, Gwinnett had ordered McIntosh to lead a poorly planned and poorly led military expedition into British Florida. The operation was a disaster and both Gwinnett and McIntosh publicly blamed each other for the failure further straining the already tenuous relationship between the two men.

On May 1, 1777, Lachlan McIntosh addressed the Georgia assembly denouncing Gwinnett in the harshest terms calling him a "scoundrel and lying rascal." Gwinnett sent a written challenge to McIntosh demanding an apology or satisfaction. McIntosh refused to apologize and Gwinnett challenged him to a duel.

On May 16, in a field owned by James Wright a few miles east of Savannah, Gwinnett and McIntosh met to duel with pistols. At a distance of 12 paces, the two men leveled and fired virtually simultaneously. Gwinnett received a ball to the hip and McIntosh was struck in the leg. McIntosh would recover from his wounds, but Gwinnett’s wound was mortal and he died three days later. Gwinnett’s allies had McIntosh charged with murder, but he was acquitted in the ensuing trial. George Washington, fearing Gwinnett’s allies would take revenge on McIntosh, ordered him to report to Continental Army headquarters on October 10. He spent the winter of 1777 - 1778 with the Continental Army at Valley Forge, Pennsylvania, where he commanded several regiments of North Carolina troops.

On May 26, 1778, McIntosh was given command of the Western Department of the Continental Army, headquartered at Fort Pitt (present day Pittsburgh, Pennsylvania) on the Pennsylvania frontier. He restored order along the frontier and conceived a plan to attack the British stronghold of Fort Detroit. He established several new forts including Fort Laurens, named for his friend and mentor Henry Laurens, who had become President of the Continental Congress, and Fort McIntosh (near present day Beaver, Pennsylvania) to prepare for the attack. The expedition against Fort Detroit was doomed however, and the troops were forced to turn back before reaching the fort.

McIntosh was replaced as commander of the Western Department by Colonel Daniel Brodhead on March 5, 1779. Washington ordered McIntosh to return to the south to join General Benjamin Lincoln in Charleston, South Carolina. He marched to Augusta, Georgia, in command of the Georgia troops, and then proceeded to Savannah, where he commanded the 1st and 5th South Carolina regiments during the siege of Savannah.

After the battle, he retired his troops to Charleston where he remained to defend the city from the British Army. On May 12, 1780, General Lincoln was forced to surrender the city to British General Sir Henry Clinton. McIntosh was taken prisoner and remained in captivity until he was exchanged on February 9, 1782.

McIntosh returned to his plantation to find it ruined by the occupying British. McIntosh tried to restore his property and business interests, but he would spend the rest of his life in relative poverty. He was elected to the Continental Congress in 1784, but never attended. In 1785, he was appointed a commissioner to treat with the southern American Indian tribes. In 1787, he was asked to help settle a boundary dispute between Georgia and South Carolina. In 1791, he was part of the delegation that officially welcomed President George Washington to Georgia.

McIntosh died in Savannah, Georgia, on February 20, 1806. The state of Georgia named McIntosh County in honor of his family. McIntosh is buried alongside his great-nephew Colonel James S. McIntosh (1784 – 1847) at Colonial Park in Savannah's historic district. His great-great-nephews, James M. McIntosh and John Baillie McIntosh, were generals on opposite sides in the American Civil War.