Input of gst in traveling through flight

But Make my trip providing GST bill and Indigo Airline also provide GST Bill, Mentioning Our GSTIN,

Which input I should go for. Please guide.

Make My Trip will provide GST invoice for the Convience charges, whil airline will provide GST invoice for airfare, you can claim ITC for both, if it is business purpose.

I know this question is old however, this might help someone else.

As indiannetizen has rightly pointed -and to elaborate on the same, both invoices are for different purposes and therefore both need to be booked as follows:

1) A GST invoice from Travel Agent (like makeMyTrip.com) will show their service charges as Taxable amount + GST on such taxable services; The Actual flight cost (charged by flight operator, in your case GoIndigo, in the separate GST invoice) is added by MakeMyTrip / Agent as purely reimbursable expense (since flight operator was paid by MakeMyTrip). Hence, GST is not levied by MakeMyTrip on the same (treated as non-taxable charges by MakeMyTrip / booking agent).

Depending on whether the agent reported the bill amount with or without reimpursable portion, (check your GSTR-2A to find out), you should book the expense entry accordingly.

2) As mentioned in point 1 above, for the Actual flight cost (inclusive of GST), you get a separte invoice from the flight operator that you should book as it is.