Which account did you use for the joint return---his or yours? You can only file it from one account. If you used your spouse's account that is where the return will be. it will not show up in your account.
Yes it will only be in your spouse's account. Hope you filed your joint return correctly. ALL of your combined income was supposed to be on ONE tax return. So your income and your spouse's income had to be on there. The refund comes in both names. Sounds like the two of you had better check it and see if you entered everything correctly. Who sat down at the keyboard to prepare it? Print it out and look at it.