Index options in the money

Yes, ITM index options are settled at intrinsic value. If Nifty is at 16050 on expiry, the 16000 Call option will expire with intrinsic value of 50, this will be credited to your account.

Also, for Long ITM Options that are left to expire, the exchange charges STT at 0.125% on the intrinsic value. You can learn more about this here: Starting Sep 1st, finally no more STT trap on exercised options :)

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