Clifford is best remembered for his apparent treachery at the second siege of Limerick. Walter Harris (qv) suggested that he was a member of a moderate party which wished to put an end to the war, and that the Irish became suspicious of him after the death (August 1691) of Tyrconnell (qv). Nevertheless Clifford retained command of a troop of horse to guard passes on the Shannon. Stationed on the Clare bank of the city, Clifford, with a mixed force of dragoons and infantry, was responsible for defending the river bank and keeping a special watch on St Thomas Island. According to Nicholas Plunkett (qv) (d. 1718), Clifford had been forewarned of General Ginkel's (qv) attempts to ford the Shannon but ‘he seemed not to give credit to any such account’ (A light to the blind). Although Plunkett acknowledged that Ginkel's force of 20,000 men could not have passed the ford if Clifford had executed his trust, he nevertheless scorned the Irish commanders who blamed Clifford for not defending the pass while they themselves gave up Limerick with even greater ease.
Writing to Walter Harris (qv), the earl of Westmeath (a Jacobite veteran) confirmed Clifford's great neglect, his subsequent imprisonment in the castle at Limerick, and the strong possibility that he would have faced a court-martial had the treaty of Limerick not been concluded. For Charles O'Kelly (qv) he was ‘vain and of shallow parts’; if innocent of treachery, he was at least guilty of unpardonable neglect; Sarsfield had been imprudent to entrust Clifford with military command, as ‘he knew him to be a creature of Tyrconnell's’ (Macariae excidium, 151).
After the conclusion of the treaty Clifford returned to Dublin and was purportedly involved in bringing Irish soldiers over to the English service.