Governance and Policy-Making
- CSG - Central Student Government
- ACES - Association of the College of Engineering Students
- ASC - Agriculture Student Council
- CITSC - Center for Integrated Technologies Student Council
- CONUS - Council of Nursing Students
- CSSC - College of Computer Studies Student Council
- SBMSC - School of Business and Management Student Council
- TG - Teachers’ Guild
- UNITASS - United Arts and Sciences Student Council
Media and Arts
- ACC - Ateneo Camera Club
- DEVCOM - SOC Development Communication Society
- XELLO - Xavier English Language and Literature Organization
- XUSELICS - XU School of Education Literary and Communications Society
- KAFIL - Kabalikat na Atenista sa Filipino
- XUAdCPDC - XU Ateneo de Cagayan Parliamentary Debating Circle
- CDA - Circulo de Arte
- Soundtable
- XU Band - Xavier University Band
- XUGC - Xavier University Glee Club
- XUCDT - Xavier University Cultural Dance Troupe
- XP - Xavier Philharmonia
- TXS - The Xavier Stage
- DA - Dulaang Atenista
- CruPub - The Crusader Publication
- CYB - Crusader Yearbook
Environment
- XUMSS - Xavier University Marine Science Society
- NC - Nature Crusaders
- XU AMS - Xavier University Mountaineering Society
Sports and Recreation
- Rodeo - Xavier University Rodeo Enthusiasts
- Bullriders - Xavier University Bullriders Association
- XU JKA - Xavier University Japan Karate Association
Natural Sciences, Engineering and Technology
- MATHSOC - Mathematics Society
- BIOPHILIC - BIOPHILIC Society
- CHEMSOC - Chemistry Society
- XCEL - Xavier Computer Enthusiasts’ League
- JPSME - Junior Philippine Society of Mechanical Engineers – XUC
- JIECEP - Junior Institute of Electronics Engineers
- IIEE - Institute of Integrated Electrical Engineers CSC-XU
- JPIChE - Junior Philippine Institute of Chemical Engineers
- PICE - Philippine Institute of Civil Engineers – XUSC
- PIIE - Philippine Institute of Industrial Engineers – XUSC
- XASED - Xavier University Association of Science Educators
- AISSA - Ateneo Information Systems Student Association
Business
- JPIA - Junior Philippine Institute of Accountants
- JMA - Junior Marketing Association
- XU ABECS - Xavier University Alliance of Business Economics Students
- JFINEX - Junior Financial Executives
- ARES - Ateneo Real Estate Service
Food and Agriculture
- AAC - Ateneo Agri-Business Circle
- ACROSS - Ateneo Crop Science Society
- ASAGE - Ateneo Society of Agricultural Economists
- JPSAS - Junior Philippine Society of Animal Science
- PAFT - Philippine Association of Food Technologists
- PSAE - Philippine Society of Agricultural Engineers – PPG XU
- PAA Jrs- Philippine Association of Agriculturists
Socio-Cultural
- ECOSOC - Economics Society
- APC - Ateneo Philosophy Club
- ADC - Ateneo Diplomatic Corps
- XUPS - Xavier University Psychology Society
- AFS - American Field Service – Xavier
- KALIWAT - Kaliwat Ki Apu Agyu
- XISA - Xavier International Students Association
Service-Learning
- XU RCY - Xavier University Red Cross Youth
- SPEDSOC - Special Educators’ Society
- XU SECT - Xavier University Society of Early Childhood Educators
- XU HUGE - Xavier University Holistic Union of General Educators
- XADSO - Xavier University-Ateneo de Cagayan DOST Scholars’ Organization
- ARC - Ateneo Rover Circle
- XU-PAF ROTC XU-Philippine Air Force Reserved Officers Training Corps
Program-Based
- STREAMS - STREAMS-Pathways to Higher Education
- ASUL - Ateneo School for Upcoming Leaders
- AAM - Atenista Ako Movement
- XUPF - Xavier University Peer Facilitators