In 1836 he returned home anxious to embark on a mission of enlightenment. Abovian's efforts were thwarted as he faced a growing and hostile reaction from the Armenian clergy as well as Tsarist officials, largely stemming from his opposition to dogmatism and formalism in the school system. Abovian was appointed as the supervisor of the Tiflis uyezd school and married a German woman named Emilia Looze (died 1870) in 1839. In 1840 he was approached by English traveler Anne Lister, who was visiting Tiflis with her partner Ann Walker. She hoped that Abovian would guide her on another expedition to Mount Ararat which ultimately did not occur. He was dismissed from the school in 1843 and was transferred to the uyezd school in Yerevan where he encountered apathy and antagonism from his colleagues and the clergy.