Jafar returned to Indonesia around 1989 and then taught at Al-Irshad Al-Islamiya boarding school in Salatiga run by Osman Yusuf Ba'isa before left for Yemen. Upon his return from Yemen in 1993 with the help of a few Salafi followers, he then set up a boarding school called Ihya Sunnah ("Preserving The Prophet's Tradition") in Degolan village in Sleman, Yogyakarta on the Waqf land endowed by a nephew of some military official at the time.