In 1825, James Gordon and Peter Weir established a distillery on the site of the former Aberlour House estate. When their business failed in 1833, the distillery was taken over by John and James Grant in partnership with the Walker brothers. When the lease ended in 1840, the Grant family moved to Rothes and built Glen Grant Distillery; Peter Weir's son became their business promoter, while the Walker brothers went to Linkwood Distillery. The present-day Aberlour Distillery was built between 1879 and 1880 by James Fleming, a local businessman who had leased Dailuaine Distillery until 1879. The new distillery was located one mile from the old site, using stones from the quarry that Thomas Telford used when building the bridge at Craigellachie. The distillery expanded in 1892, and ownership was transferred to the blending firm R. Thorne & Sons of Greenock. In 1898, the distillery was destroyed by fire and subsequently rebuilt. The next owners were the English company W.H. Holt & Sons, who purchased Aberlour in 1921 and operated it for 20 years. In 1945, it was acquired by S. Campbell & Son, who modernized the facility in 1973 by installing four stills, and sold it the following year to Société Pernod Ricard. Pernod Ricard retained Campbell Distillers as its whisky division until the 2001 acquisition of Seagram's, which included Chivas Brothers, the latter assuming control of all distilleries. Since 2000, sales of Aberlour single malt whisky have increased dramatically, particularly in France. The brand is currently the sixth best-selling whisky brand worldwide. In August 2002, the distillery opened a new visitor center offering a two-hour guided tour.

Until the 1990s, the distillery was entirely water-powered. Within the distillery grounds stands a holy well dedicated to St. Drostan, a follower of St. Columba who visited Speyside around AD 660. Legend has it he used this well water to baptize the local inhabitants. He later founded a monastery at Deer in Aberdeenshire, where he wrote the famous 'Book of Deer'. In 1931, the Ross family specially built a small chapel dedicated to this saint. Ian Mitchell, who passed away in 1992, worked at the distillery for 48 years, serving as distillery manager for the final 27 years. His grandfather, father, and brother also worked at the distillery. Aberlour's 'A'bunadh' series (Gaelic for 'origin') was launched in 2000. This is a cask strength, non-chill filtered Speyside product. As of 2019, 64 batches have been released. Aberlour House is now the headquarters of the famous shortbread brand 'Walkers of Aberlour'.