We have a customer that has one DBA account with us however he makes deposits from two businesses into the account. Both are owned by him and of the same nature business. Since the DBAs are both under his TIN, is it ok for him to deposit checks made out to both businesses into an account with only one of the businesses name on it?

I believe you should add the other business name to the account as well (if your bank is willing to do that.) You could also take the stand that they need to open a separate account for the separate business.

Do you have documentation that the customer is registered to do business under each of those names?

When you have a DBA account, checks made payable to the person (owner) or to the business can be deposited into that DBA account. I would not deposit checks made payable to another business into the account. He should be required to open another account for the other business.

Whether your bank will permit the additional business to share the account is a matter for your bank's policy. There's no legal requirement one way or the other. Your customer would obviously prefer to have only one account and one monthly service fee. That may not be in your bank's best interest, however.