How can the user fee for an exemption application be paid?
If the organization is submitting Form 1023, the fee may be paid by check or money order payable to United States Treasury.
If the organization is eligible to submit Form 1023-EZ, the fee must be paid through www.pay.gov when the application is filed. Payment can be made directly from your bank account or by credit/debit card.
The IRS will not process an application until the user fee has been paid.