On 13 December 1896, just ten days after she was launched fully rigged and seaworthy, her maiden voyage brought her in ballast to Liverpool and from there with a general cargo to Portland, Oregon.

For 23 years she traded as a bulk cargo carrier under the Red Ensign via Cape of Good Hope to Australia, returning via Cape Horn, firstly under the ownership of Archibald Sterling and Co, Glasgow, then as Islamount of Islamount Sailing Ship Co Ltd (Robert Ferguson & Co), Dundee (1898–1905), and finally with the Flint Castle Shipping Co Ltd (Robert Thomas & Co), Liverpool (1905–1918).

In 1990 a British naval architect (Dr. Sir John Brown, 1901–2000) discovered the ship and in 1993 she was rescued from being scrapped and subsequently bought by the Clyde Maritime Trust at auction for 5,000,000 ₧ or £40,000.

After preliminary works in dry-dock such as the removal of the unnecessary propellers, the check and repair of all the plates below the waterline and new paint, a six-year-long process of restoration began including a new cut wooden figurehead, a complete set of new rigging including the re-assembling and re-stepping of her original masts and re-crossing of the old yards (1998), as well as many other replacements (original deckhouses) and repairs.

Her old masts and many of the old yards, which still existed somewhere in Spain, were returned by the Spanish when they realised that the old ship would be really renewed to her original "Cape Horn status", painted grey again with "gun ports".

[clarification needed] Her propellers are now situated in the courtyard by the yard arm of the City Of Glasgow College, Nautical Faculty by the River Clyde.

All changes made to the ship by the Spanish and previous owners were to be removed, such as all the cabins built for the trainees and the scrap iron ballast in the frames of the holds.

As a museum ship and tourist attraction, Glenlee offers educational programmes, events including exhibitions and is a venue for the West End Festival and volunteering opportunities.