Shaffi joined NSU (Kerala – KSU) in 1985 at Sacred Heart College, Cochin, India. He was a very active leader on campus.

In 1987, he joined St. Pauls College for his undergraduate degree course and soon became one of the key leaders of KSU at St. Pauls College. In 1988-89, he won as the University Union Councilor from St. Paul’s College to Mahatma Gandhi University Students Union defeating his opponent Mr. P Rajiv from SFI (Students Federation of India) by a huge margin.

In 1989, Shaffi was elected to the Executive Committee of Mahatma Gandhi University Students Union from the KSU panel.

In 1989-90, Shaffi led the KSU panel in St. Pauls’ College to an unprecedented victory in the College Student Union elections sweeping the elections defeating SFI winning all general and class representative seats. Shaffi himself was elected as the Chairman of the College Students union with one of the biggest majorities in the Student Union Electoral history in the State.