I'm being charged for taxes we are already paying. How do I remedy this with Shopify billing?

Accounting & Taxes

Topic summary

A merchant discovered unexpected sales tax charges on their Shopify billing statements, appearing as small amounts (e.g., $0.02, $0.28) that seemed duplicative of taxes already collected and remitted to states where they’re registered.

The Issue:

  • Monthly billing showed random tax charges, primarily for their home state (North Carolina)
  • These appeared separate from the sales tax already collected on orders and paid to registered states
  • The merchant had to manually cross-reference billing exports with order numbers to identify which transactions triggered the charges

Resolution:

  • The original poster resolved their issue by contacting Shopify support via chat, which escalated the concern to the tax team
  • A Shopify Community team member suggested reviewing Tax Overrides settings for better control over the tax system

Ongoing Question:

  • Another merchant (MissyP2) reported similar unexplained Louisiana sales tax charges appearing on their Shopify bill starting in January, with an attached screenshot showing the charges
  • This suggests the issue may affect multiple merchants across different states
Summarized with AI on November 1. AI used: claude-sonnet-4-5-20250929.
1

Each month I get and email that Shopify has charged my account. Sales tax…I understand once I reach a threshold of orders or sales that I have to register with that state and enter my account number in Shopify so they start charging and we start paying that state.

When I go to Billing in my account and see Shopify has charge a random amount to our credit card and export the billing fees I then have to put the number from Column K into the search bar in “orders” in Shopify and I can find the order #. From there I see what state the order is from and that we charged tax for the state and county and we have paid the sales tax to our accounts registered in those states. SO why are we being charged twice? Our business is located in NC and we’ve been paying taxes here for decades…this past billing cycle most of the exported “billing” charges are in NC. These are odd totals too such as .02 or .28. This has been going on for months and it’s hard to get support form anyone with Shopify. My accountant and I are very frustrated.

Lynn R.

2

Hi, @lynnruck .

Rio here from the Shopify Community team. I understand your concern about the sales tax charges and I’m here to help.

To better assist you, could you please provide me with the following information:

  1. Are these charges appearing for all orders or only for certain states?
  2. Have you recently made any changes to your tax settings in Shopify?

Once I have this information, I can provide a more targeted solution.

I believe what you’re looking to do is set up Tax Overrides. Tax overrides allow you more control over your tax system with Shopify. I recommend going over that, then speaking with your accountant so you can implement it the correct way you need.

3

Hello, This has been resolved. I was able to chat with a person that
escalated our concern to the tax team.
Thank you, Lynn

4

Can you tell me what these charges are (Louisiana sales tax) for on my shopify bill? I just started seeing them show up in January.

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