A Royalist during the Civil War, he returned to service after the Restoration and eventually rose to the rank of Admiral of the White after serving under some of the most distinguished military figures of the era, including Prince Rupert of the Rhine.

[2] During 1663 he was made Commander-in-Chief, the Downs with the rank of commodore, flying his pennant aboard HMS St Andrew from 15 April 1664.

Rupert retained Allin as his first captain for this assignment, but the intelligence was proved to be false, and no French fleet was found.

Rupert and Allin hurried back and met up with the harried and outnumbered English fleet on the third day, managing to hold the Dutch off long enough to allow a successful disengagement and then covering the retreat.

[1] He returned to England after this and on 15 April 1671 he became Comptroller of the Navy, a post he held throughout the Third Anglo-Dutch War and continued to hold until 28 January 1680.

[2] He briefly returned to active service in 1678 when the threat of war with France emerged, and Allin became commander in chief of the fleet in the Narrow Seas, with HMS Royal James as his flagship.