Allegiance Pays Through Zelis — How to Avoid the ~3% Virtual Card Fee
By George Ruan • June 26, 2026
If Allegiance is paying you through Zelis, you're likely losing 2–3% of each payment to a fee. Bomi switches you to no-fee direct deposit so you keep the full amount.
Allegiance delivers its provider payments through Zelis. Allegiance Benefit Plan Management is a third-party administrator (TPA), and its payments run through Zelis. When a payment arrives as a Zelis virtual card (a single-use card number you “redeem” in your merchant portal) or a fee-based “fast” EFT, running it skims a 2–3% processing fee straight out of your payment.
You don't have to pay that fee
Federal CMS guidance is clear that a health plan or its vendor cannot require you to accept virtual cards, and that you can request the no-fee standard ACH EFT instead. The 2–3% is a charge for an optional service you can decline. (For the full legal basis — the HIPAA EFT standard adopted under the Affordable Care Act — see our Zelis no-fee EFT guide.)
How to switch for Allegiance
Opt out of the virtual card with Zelis, and don't run any card in the meantime (running it is what charges you).
Enroll in no-fee standard ACH EFT for Allegiance, through its payer-sponsored Zelis ePayment Center, using your practice TIN/EIN, NPI, and bank account.
Set up electronic remittances (835/ERA) so payments post cleanly in your system.
If they resist, file a CMS Administrative Simplification (ASETT) complaint naming the plan — they can't condition electronic payment on a fee.
How Bomi helps
Bomi handles Allegiance for you: we opt your practice out of Zelis virtual cards, enroll you in Allegiance's no-fee standard ACH EFT, and set up your electronic remittances so payments post cleanly. You stop losing the 2–3%.
This article is general information, not legal advice. The protections described come from federal CMS guidance and your right to request the standard EFT transaction; enforcement runs through the CMS complaint process, and specifics can change. Confirm your options with the payer and CMS before relying on them.
Want us to get the virtual-card fees off your payments? Reach us here https://www.billwithbomi.com/#contact.
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