Rubuta ci gaba don wannan sakin layi - Kwalejin ta sha wahala mai yawa da asarar jari a lokacin mamayewar Sweden na 1656
da annobar annoba ta 1710, amma ya warke. Bayan murkushewa na Jesuits a 1773, Hukumar Ilimi ta Kasa ta karɓi kulawar kwalejin. Bayan Raba na Uku na Yaren mutanen Poland-Lithuanian Commonwealth, Carmelites daga Kolainiai sun gudanar da makarantar daga 1797 zuwa 1817. A cikin 1817, hukumomin Tsarist sun lalata makarantar, sun canza sunanta zuwa makarantar motsa jiki, sun gabatar da azuzuwan ilimi na farko, kuma sun canza gwamnatinsa zuwa Jami'ar Vilnius. Saboda haka, yawan ɗalibai ya ƙaru kuma ya wuce 400.