Destiny Church started in 1998 as a prayer meeting held by a student group called Students for Christ within the University of the Philippines, Los Baños. From 15 members, it grew to over 300 students.
In 1998, Pastor Leo Carlo Panlilio, together with his wife, Pastor Zhaleen Panlilio, set out to Quezon City in the hopes of replicating the movement they started at UP Los Baños to its QC campus, University of the Philippines, Diliman. In its first few years, Destiny Church held services in different locations: at the Manor Hotel at Kamias Road, King’s Court, Chicken Bacolod at Quezon Memorial Circle, and Camelot Hotel among many others. Now, Destiny Manila has given birth to three satellites in the metro; Destiny South at Parañaque, Destiny North at UP Diliman, and Destiny Central at Ortigas.