On the outbreak of the war with France in 1793 he was appointed to command of Hotham's flagship, the 100-gun , seeing action at the siege of Toulon. Following the recall of Admiral Samuel Hood in late 1794, Hotham became Commander-in-Chief of the Mediterranean Fleet, and Holloway became his Captain of the Fleet. As such he took part in the Battle of Genoa in March 1795 and the Battle of Hyères Islands in July. At the end of the year Hotham was replaced by Admiral Sir John Jervis, and Holloway was appointed to command of the 98-gun . He was present in her at the Spithead Mutiny in May 1797, and afterwards commanded , attached to the Channel Fleet.