Difficulties experienced by the army under the Prince of Anhalt were further complicated by the deaths of those supporting it financially and politically. Setbacks and obstacles were nothing new to Elizabeth's relationship with the Protestant Princes, but these impediments were significantly more challenging than those before. From 1592 forward, theological and political disputes around the Empire needed resolution before a coherent foreign policy in any given area could be re-established with England. Across the Channel, Elizabeth and Burghley recognized the implications of these events, and the English quickly became comparatively lonely in what five years previously was a much broader Protestant world. With German and English Protestant leadership looking inward to their own estates, Anglo-German military operations and diplomacy effectively ceased. This retreat left Henri IV without any prominent friends in the Empire and with staggering debts to a penny-pinching and aging Elizabeth. Henri's only remaining option to gain Paris and bring peace, therefore, was to submit to the Catholic League. On 25 July 1593, he officially converted to Roman Catholicism at the Abbey of Saint-Denis and soon entered Paris to take Mass at Notre Dame. The decline in Anglo-German collaboration after Rouen may not have been the main reason for Henri's capitulation, but it was a contributing factor.

These developments represented a watershed in the confessional conflicts of mainland Europe.