A lokacin da karni na 16 yana wucewa, marigayi dan Adam ya shiga tare da Calvinism a matsayin babban makarantar tunani; kuma mutane kamar Paul Schede, Jan Gruter, Martin Opitz, da Matthäus Merian sun koyar a jami'ar. Ya jawo hankalin malamai daga ko'ina cikin nahiyar kuma ya ci gaba da zama cibiyar al'adu da ilimi. Duk da haka, tare da farkon Yakin Shekaru talatin a 1618, dukiyar ilimi da dukiyar jami'ar ta ragu. A shekara ta 1622, an sace Bibliotheca Palatina (littafiyar jami'ar) daga Jami'ar Jami'ar kuma aka kai shi zuwa Roma. An sake sake sake kokarin sake gina shi daga sojojin Sarki Louis XIV, wanda ya hallaka shi a shekara ta 1693. A sakamakon ƙarshen Counter-Reformation, ɗaliban jami'ar Protestant sun rasa halinsa, kuma Matthäus Merian ya koyar da shi a jami'ar.
ilimi da kuma kudi arziki na jami'a ya ragu