APTS is known for being accredited by theological agencies associated with all three main branches of the Protestant Christian Family:
Association for Theological Education in the Southeast Asia (ATESEA) – Liberal

Master of Divinity (M.Div)
Master of Arts Degrees (M.A.)
Master of Theology (M.Th.)
Asia Pacific Theological Association (APTA) – Pentecostal/Charismatic
Master of Divinity (M.Div)
Master of Arts Degrees (M.A.)
Master of Theology (M.Th.)
Asia Theological Association (ATA) - Evangelical

Master of Divinity (M.Div)
Master of Arts Degrees (M.A.)
Master of Theology (M.Th.)
APTS also recently received 5 degree recognitions from the Philippine Commission on Higher Education (CHED).
Commission on Higher Education (CHED)

Master of Divinity (M.Div)
Master of Arts in Intercultural Studies – Islamic Concentration (M.A.I.S)
Master of Arts in Ministry (M.A. Min.)
Master of Theology (M.Th)
Doctor of Ministry (D.Min)