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The phrase cujus regio, ejus religio has frequently been used in order to reference the mapping of confessions in the Holy Roman Empire throughout the early modern period: allegedly, each prince imposed his religion on his territory. Undoubtedly, the confessional mapping during the 16th century was partly determined by princely decisions in the Empire. However, this Latin phrase does not do justice to the complexity of a disputed situation; furthermore, the Peace of Westphalia in 1648 rendered the phrase quite irrelevant. The “normal year” (1624) rule indeed “froze” the confessional borders, even though interpretations diverged concerning the implementation of this rule. Conversions of princes were still frequent after 1648 (it was the case in Saxony, Wurttemberg and, through inheritance, in Palatinate) and they resulted in a separation of the prince’s religion from his territory’s confession, as well as in an empowering of local confessional identities. This paper provides a survey of key elements (especially legal ones) inscribing the evolution of princes’ conversions into the genuine political and confessional frame of the Holy Roman Empire during early modern times, and emphasizing how intertwined were local conflicts, territorial powers and imperial regulations.