On August 16, 1593, Tobie set sail from London headed for Zakinthos and Patras in Greece via Livorno. For the ship's master, George Goodlay, this was his first voyage as master on a Levant route. Writer Richard Hakluyt adopted a dim view of him, lamenting "being a young man, and one which never tooke charge before for those parts, was very proud of that charge which he was litle able to discharge, neither would take any counsel of any of his company, but did as he thought best himselfe".
Tobie proceeded down the English Channel and called at Portsmouth to take on a load of wheat. On October 6, it departed the Isle of Wight, where conditions were described as fair, and twelve days later approached the Strait of Gibraltar, where foul weather threatened to run the ship aground, forcing the crew to sail back out to sea.
On the night of October 19, an attempt was made to transit the strait. Still, Goodlay had incorrectly calculated their position, and Tobie ran aground approximately an hour and a half before dawn. Tobie was carrying sail at the time, regarded as an ill-advised action on an unfamiliar coast at night. The ship's estimated position was 12 miles (19 km) south of Cape Spartel.
Goodlay immediately accepted the responsibility to his crew, stating, "I pray you forgive me; for this is my fault and no mans else." They wished to cut the main mast to reduce the strain on the ship's timbers, but Goodlay sought to launch a boat instead. However, upon learning of the depth of the water in the hold, he assented to their plan. This action was then precluded by the ship's breaking in two.
The crew began to sing Psalm 12 as they desperately clung to the mast, which collapsed before the end of the fourth verse, flinging the men into the water. Of the ship's crew of 50, 38 drowned before being able to reach the shore about a quarter of a mile (400 m) away. The few survivors avoided death by clinging to flotsam or swimming. Goodlay and his mate, William Palmer, were among the dead. The ship's carpenter, William Williams, was the sole surviving officer.