Nor were they cut off from political events at home. Two granddaughters of the Gunpowder plotter Ambrose Rookwood became abbesses of Poor Clare convents, one at Gravelines, the other at Dunkirk. The family of Richard Weston, 1st Earl of Portland and Charles I's lord treasurer, had dealings with the convents, acting as patrons and some entering the English Poor Clare convent at Rouen and the Sepulchrine establishment at Liège. The exiled women religious were not immune from the internal Catholic political arguments of their homeland, such as over the best way to proceed when dealing with a state that indulged in periodic bursts of bloody oppression. Indeed, the Benedictine establishment at Brussels nearly fell apart as these external disagreements coloured other issues festering inside the convent's walls.

The advent of the English Civil War in the middle of the 17th century brought a new dimension to the convents' existence as the Stuarts fled into exile with their surrounding court. Kent-born Mary Knatchbull was a formidable figure. Abbess of the English Benedictines at Ghent, she founded three daughter houses from that one convent — at Ypres, Dunkirk and Boulogne (which later moved to Pontoise and was the only convent to fail in exile, a testament to the general level of the nuns' financial acumen). During the 1650s, she developed close relations with Charles II's court in exile. She provided hospitality for the royal entourage and used the convent as a "clearing house" for the mail of key royal advisers. She possessed a wide network of contacts both at home and abroad and she shared information with the royalist campaigners. Knatchbull also lent substantial sums of convent money to the cause and even offered the king advice on the best way to proceed once the Restoration was announced. On his way "home" in 1660, Charles called at the convent to say goodbye and repay a little of the money. The rest was never forthcoming, despite Mary Knatchbull undertaking several trips to London in an effort to recover the remainder.

When the Stuarts once more headed into exile following William of Orange's  arrival during the "Glorious Revolution" of 1688, the convents had a role to play in Jacobite affairs. Their schools, such as those of the Paris-based English Augustinians and Conceptionists, provided education for the children of exiles. They also allowed the Stuart court to act in a manner befitting a Catholic monarch on the continent, members of the household paying visits to the convents and even attending clothing ceremonies, when young women would receive the habit. For some of the convents, the Catholic cause merged with that of the Jacobites. The Paris Augustinians cherished as a relic of a martyr the heart of James Radcliffe, 3rd Earl of Derwentwater, who had been executed following his leading role in the 1715 Jacobite rebellion.

With the Jacobites' final defeat following the 1745 rebellion, the real chance of reclaiming the country for Catholicism dissipated in England. Like their fellow nationals back home, the convents felt the squeeze of entrenched Protestantism through declines in income and numbers. Though convent membership was not the sole preserve of the elites, there appears to have been a shift in the later 18th century towards more "common" Catholics.