At the beginning of 1583, Stanley was sent back to Ireland to deal with the rebel Geraldines of Desmond, and was appointed by the Earl of Ormond as commander of the garrison at Lismore; he was also constable of Castlemaine, which he intended to ""make a town of English"". During this tour of duty he assisted in the pursuit of the earl of Desmond and James Fitzedmund Fitzgerald, the seneschal of Imokilly, and in the final subjugation of Munster at the end of the rebellion.