It will be considered as on time payment, but could have 20-30 point impact on the credit score. As banks always charge the interest, it's the seller who gives upfront discount of interest value at payment time.
if you have cash lying around, call the cc company and pre-close the emi you'll get to pocket the interest difference.
For example.
₹100000 item bought at no cost emi of 6 month will be billed as ₹93000 on your cc, bank will then take monthly installments in breakup as 15500 principal + 1200 interest + 200 gst on interest, summing up to little over 100k
If you cancel emi and pre pay the outstanding you'll only have to pay 93000k + 500-1000 fee, cancelling emi can also be free if done within a week