Glen Moray was built on the site of the West Brewery to the west of Elgin on the banks of the River Lossie. Following reconstruction, Glen Moray Distillery was founded in 1897. It was not long before the distillery closed in 1910, though it reopened a couple of years later, shortly before closing once more. In 1920, Macdonald and Muir acquired the distillery and once more spirit flowed from the stills. The distillery operated its own floor maltings, converting to a Saladin Box in 1957, which remained in use until 1978. During the 1970s, the two original stills were replaced and two further stills were added, giving the distillery a total yearly capacity of two million litres.

In 1996 Macdonald and Muir Ltd renamed itself Glenmorangie Plc and in 2004 the group was acquired by Louis Vuitton Moët Hennessy, for the princely sum of £300 million. The Glenmorangie distillery pioneered exotic wood finishes and Glen Moray championed white wine finishes, releasing a Chardonnay finish and two Chenin Blanc finishes in 1999.

Most of the whisky from Glen Moray has long since been used in blended Scotch. More recently, the Glenmorangie Co decided to cease producing whisky for blending and subsequently, in 2008, the distillery was put up for sale. There are several official house bottlings, but independent bottlings are rather rare.