Quarterly Sales Tax Filing Checklist

Why Quarterly Filing Matters

Most states assign quarterly filing frequency to medium-volume sellers. If you're collecting sales tax in multiple states, staying on top of quarterly deadlines is essential to avoid penalties, interest charges, and compliance headaches.

30 Days Before Filing: Preparation Phase

1. Review Your Nexus Status

Before each quarter, check if you've established nexus in any new states. Use our Nexus Checker to see if you've crossed any new thresholds.

Action items:

• Download sales reports from all platforms (Shopify, WooCommerce, etc.)
• Calculate total sales by state for the quarter
• Register for permits in any new nexus states
• Note which states require filing (even if no tax collected)

2. Gather Your Sales Data

Compile sales data from all channels. Remember: you only report sales where you collected the tax, not marketplace sales where Amazon/Etsy collected it.

What to collect:

• Gross sales by state
• Exempt sales (resale certificates, tax-exempt customers)
• Tax collected by state/local jurisdiction
• Shipping charges (taxable in most states)
• Refunds or returns issued

3. Organize Exemption Certificates

If you made wholesale sales or sold to tax-exempt organizations, make sure you have valid exemption certificates on file. Most states require these in case of audit.

Certificate checklist:

• Verify certificates are signed and dated
• Confirm certificates cover the correct time period
• Match certificate numbers to exempt transactions
• Store certificates securely (digital + backup)

15 Days Before Filing: Calculation Phase

4. Calculate Tax Owed by State

For each state where you have a filing obligation, calculate the total tax you collected during the quarter. Use our Quarterly Tax Estimator to automate this process.

5. Break Down by Jurisdiction (if required)

Some states require you to report tax by county, city, or special district. This is especially common in:

• Colorado (home rule jurisdictions)
• Alabama (county and city breakdown)
• Louisiana (parish breakdown)

If your state requires this, use your sales platform's detailed reports or tax software to break down collections by local jurisdiction.

6. Reconcile Your Records

Cross-check your calculations against bank deposits and accounting records. The tax you collected should match what's in your bank account (minus any outstanding).

Red flags to investigate:

• Sales tax collected doesn't match calculated amount (check for refunds)
• Unexplained gaps in sales data (missing transactions?)
• Exempt sales without certificates (get them now!)

5 Days Before Deadline: Filing Phase

7. Log Into Each State Portal

Every state has its own online filing portal. Make sure you have your login credentials handy. If it's your first time filing, you may need to set up an account.

8. Complete Each Return

Work through each state's return methodically. Most returns ask for:

• Total gross sales
• Exempt sales (with reason codes)
• Taxable sales
• Tax rate(s) applied
• Total tax collected
• Any deductions or credits
• Net tax due

9. Review Before Submitting

Before hitting "Submit," double-check:

• ✓ All numbers are accurate
• ✓ Exempt sales have valid certificates
• ✓ Math adds up correctly
• ✓ Bank account info is current (for ACH payment)
• ✓ You're filing for the correct quarter

10. Make Your Payment

Most states allow electronic payment via ACH, credit card, or e-check. Pay immediately after filing to avoid missing the deadline.

Payment methods ranked:

1. ACH (best): Free, direct from bank account
2. E-check: Free or low fee
3. Credit card: Convenience fee (2-3%), but earns rewards

After Filing: Record-Keeping Phase

11. Download Confirmation Receipts

Save proof of filing and payment for each state. Download PDFs of:

• Filed return
• Payment confirmation
• Confirmation number

Store these in a dedicated folder (e.g., "Q2-2025-Sales-Tax-Returns"). Keep for at least 3-5 years.

12. Update Your Filing Calendar

Mark the next quarter's deadline on your calendar. Set reminders for:

• 30 days before (start preparation)
• 15 days before (begin calculations)
• 5 days before (file and pay)

Use our Sales Tax Calendar to track all your state deadlines in one place.

13. Reconcile Your Books

Update your accounting software to reflect:

• Sales tax liability paid (reduce liability account)
• Payment made (reduce cash account)
• Quarterly filing complete (for your records)

State-Specific Quirks to Know

Zero-Dollar Returns

Many states require you to file even if you collected no tax that quarter. This is called a "zero-dollar return." Don't skip filing—file with $0 to stay in good standing.

Local Tax Jurisdictions

States like Colorado and Alabama have local jurisdictions that require separate filings. This can mean filing multiple returns per state. Check your state's requirements carefully.

Prepayment Requirements

Some states (like Florida and Tennessee) require prepayment if your quarterly liability exceeds a certain amount. Set aside funds throughout the quarter to meet these requirements.

Different Quarter Definitions

Most states use calendar quarters (Jan-Mar, Apr-Jun, etc.), but some states use fiscal quarters. Verify your state's quarter definition when filing.

Tools to Streamline Quarterly Filing

1. Sales Tax Software

Consider using automation tools for multi-state filing:

• TaxJar: Automated filing and remittance ($19-$99/mo)
• Avalara: Enterprise-level automation (custom pricing)
• TaxCloud: Free basic filing

2. Our Free Tools

• Quarterly Tax Estimator – Calculate tax owed by state
• Sales Tax Calendar – Track all filing deadlines
• Calculation History – Review past calculations

Complete Quarterly Filing Checklist

Common Filing Mistakes to Avoid

Mistake #1: Filing Late

Late filing penalties can be steep—5-10% of tax owed per month in many states. Don't wait until the last day. Aim to file at least 3-5 days early to avoid technical issues.

Mistake #2: Reporting Marketplace Sales

Don't include sales where Amazon, eBay, or Etsy collected the tax. Only report sales where YOU collected the tax directly.

Mistake #3: Forgetting to File Zero-Dollar Returns

Even if you didn't collect any tax in a state that quarter, you may still need to file. Check each state's requirements.

Mistake #4: Mixing Personal and Business Expenses

Keep business and personal finances separate. This makes reconciliation much easier and protects you in case of audit.

Mistake #5: Not Keeping Backup Documentation

Keep detailed records of every transaction, exemption certificate, and calculation. In an audit, documentation is everything.

When to Hire Professional Help

Consider hiring a sales tax professional if:

• You're filing in more than 5 states
• You have complex exemption situations (wholesale, manufacturing)
• You're facing penalties or audit notices
• Your quarterly liability exceeds $10,000
• You don't have time to manage filing yourself

A CPA or sales tax specialist typically charges $200-$500 per state per quarter, but the peace of mind and accuracy may be worth it.