After the outbreak of the Monmouth Rebellion, Bertie and his half-brother Richard were commissioned captains on 18 June to raise independent troops of horse. On 21 June, Henry led the troop of Oxfordshire militia horse out of Oxford toward Dorchester and Abingdon to act against the rebels in Somerset, while Abingdon raised his troop on his behalf. The troop was disbanded in December; the independent troops that were not incorporated into existing regiments were disbanded after the collapse of the rebellion, Wood records that Henry and Richard were among the officers deprived of their commissions for voting in the House of Commons in favor of the address to James II against employing Roman Catholic officers. Sometime after 1685, he was appointed a justice of the peace for Buckinghamshire. Like his brothers, Bertie belonged to the High Tories who were alienated from the court by the pro-Catholic policies of King James. In 1687, he lost his militia commission, his deputy lieutenancy, and was removed from the commission of the peace in Oxfordshire.