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1. St. Pauls College

Shaffi graduated from St. Pauls College, Kalamassery, India in March 1990 specializing in Accountancy. He graduated with First Class Honors.

At St. Pauls’ College, he was a key leader of the National (Kerala) Students Union, the student wing of the Indian National Congress. Shaffi was elected as the University Union Councilor from St. Pauls’ College in 1988-89 and as the Chairman of the St. Pauls College Union in 1989-90. He was one of the most popular Student Union Chairman in the history of the College.

St. Pauls College is an affiliated college under the Mahatma Gandhi University, also known as MG University, Kottayam, India. The Mahatma Gandhi University (formerly Gandhiji University), has been accredited by the National Assessment and Accreditation Council, India. The University has 223 affiliated colleges spread over five districts in central Kerala and is funded by the University Grants Commission and Government of Kerala. It is a member of the AIU and the Association of Commonwealth.

2. Sacred Heart College

Shaffi completed his 11th & 12th grades (then known in Kerala, India as 'Pre-Degree Course') from Sacred Heart College, Thevara, Cochin, India. Shaffi graduated from the Pre-Degree course with First Class Honors and studied Accounting & Commerce as the elective course. Shaffi formally joined National (Kerala) Students Union, the student organisation of Indian National Congress in 1985 while being a student at Sacred Heart College.

Sacred Heart College, Thevara, enjoys the privilege of being one of the best colleges under the Mahatma Gandhi University with a consistently outstanding performance record and accredited with FIVE STAR and re-accredited with A+ grade by the NAAC. It was established in 1944 by the Sacred Heart Monastery, Thevara, Cochin, a unit of the CMI (Carmelites of Mary Immaculate) Congregation, which is a Catholic religious order for men. The college has been selected by the UGC as a College with Potential for Excellence. The College has 11 undergraduate courses, 10 postgraduate programmes and 6 Research Centres.