APTS has received multiple degree recognitions from Commission on Higher Education (CHED) for the following degree programs:
- Master of Arts in Ministry
- Master of Arts in Intercultural Studies with Islamic Concentration
- Master of Divinity
- Master of Theology in Pentecostal/Charismatic Studies
- Doctor of Ministry in Pentecostal/Charismatic Ministries
Aside from that the APTS Master of Divinity and Master of Arts degree programs are accredited by the Association for Theological Education in South East Asia (ATESEA), the Asia Theological Association (ATA), and the Asia Pacific Theological Association (APTA).
Accreditation for the Master of Theology in Pentecostal Studies program has been arranged with the Association for Theological Education in South East Asia (ATESEA). Accreditation for the Doctor of Ministry (D.Min.) is granted from ATA and APTA.