[4] By then a widower, Bowes strengthened his position by an alliance with the powerful house of Shrewsbury, when he married Jane, daughter of Sir John Talbot of Albrighton.

In 1569 the Rebellion of the Northern Earls threatened Elizabeth's throne, and he played a major part as a loyalist, remaining at Streatlam and facing down unpopularity.

On 7 March, Henry Carey, 1st Baron Hunsdon wrote, "The country is in great hatred of Sir George Bowes so as he dare scant remain there".

At length their proceedings were so threatening that Bowes on 12 November left Streatlam, and shut himself up in Barnard Castle, which belonged to the crown and of which he was steward, with forces levied for Queen Elizabeth and gentlemen of the neighbourhood.

He wished to use this small force for the purpose of cutting off the rebels who were gathering at Brancepeth; but Sussex hesitated to give permission, and things were allowed to take their course.

On 14 November the rebel Earls entered Durham, and advanced southwards for the purpose of releasing Queen Mary from her prison at Tutbury; but they did not agree internally, changed their plan suddenly, and retreated northwards.

Bowes held out for eleven days, but fearing treachery within he made a surrender on honourable terms, and marched out with four hundred men.