Catholic opposition in England was made more of a threat by the hostile international political situation which allowed insurgents to gain foreign support and led to plots against Elizabeth's life. On the other hand, Puritan opposition gained no foreign support and was largely confined to nonconformity in individual parishes, displaying little organised opposition against the crown. While Haigh has argued that Elizabeth and her Council "overestimated the Catholic threat" due to the inefficacy and poor organisation of missionary activity, Susan Doran has argued that missionares were very effective as proselytisers. An increase in measures taken against missionary and Jesuit priests can be seen to reflect their increasing threat to the stability of Elizabethan power, resulting in Elizabeth's own heightened paranoia. While Elizabeth's efforts to conciliate lay Catholics in the 1560s meant that by the arrival of the first Jesuit priets in 1580 the majority of Catholics had "drifted into conformity", as Susan Doran has argued, her concessions had the effect of alienating Protestant ministers and councillors. However, nonconformity in parishes would prove to be the extent of the Puritan threat, which cannot compare to the Catholic threat of foreign invasion in the Throckmorton Plot of 1583 and Babington Plot of 1586, which gained Phillip II of Spain’s support.
Catholic opposition was far more organised than Puritan opposition, posing a real threat to Elizabeth. much of the missionary activity was misdirected because they focused on the South East of England, which was mostly Protestant, and restricted themselves to gentry households it made sense to target the leaders of communities with wider spheres of influence and to choose areas close to London in which to operate as an obvious focal point for activity. This organisation of the Catholic mission has led Bossy to argue that in 1574, “the arrival of Priests did much to ensure the survival of an English Catholic community”. This, very real, threat is reflected in the increase in recusancy from 1574. The organisation of Catholic plots against the Crown went further than nonconformity, with twelve conspirators committed to murdering Elizabeth in the Babington Plot of 1586 as well as the attempt of leading Northern nobles to overthrow Elizabeth in the Northern Rebellion of 1569, which was led the Earls of Northumberland and Westmoreland and Lord Dacre. The closest thing to organised opposition from Puritans can be seen in the refusal to conform to Elizabeth’s repression of prophesying. However, as Collinson argues, Elizabeth didn’t feel threatened by prophesyings she just didn’t see the need for more than 3 or 4 preachers per county. Therefore the foreign element and higher levelsof organisation of the Catholic threat meant that Catholics posed more of a threat to Elizabeth than Puritans did.