GST will not affect your loan repayments. Before the introduction of GST, service taxes were being levied on loans. The rate of service taxes were 15%, whereas the rate of GST is 18%. People might think that the EMI costs will be affected because the rate of GSTs increased by 3%. But GST is not levied on repayment of the loan or on the payment of interest on the loan. It will be levied only on the processing charges and other charges that your lender would be imposing, excluding the repayment amounts and the interest amounts. Charges like the loan processing charges or the prepayment charges. 

Some people might even think that their EMIs will go up due to GST. For example, assume your lender levies a processing fee of 1% on your personal loan amount. Your loan amount is Rs. 9 lakhs, therefore you would have to pay Rs. 9000. On this amount, when 18% of GST is charged, you would have to pay an additional amount of Rs. 1,620.