What Happens After You File Your CT600? HMRC Processing Timeline

What Happens After You File Your CT600? HMRC Processing Timeline

You've filed your CT600 corporation tax return. Now what? Many directors submit and then wonder: did it go through? Will I hear back? What if something's wrong?

Here's exactly what to expect after filing.

Immediate Response: The IRmark

When you submit your CT600 through filing software, HMRC's system validates the submission immediately. Within seconds, you'll receive one of two responses:

Successful Submission

• An acknowledgement with a unique correlation ID
• This confirms HMRC received your return
• Your filing software should show a "submitted" or "accepted" status

Rejection

• An error message explaining what's wrong
• Common reasons: invalid XML, missing mandatory fields, incorrect IRmark
• You'll need to fix the issue and resubmit

Important: A successful submission acknowledgement does NOT mean your return has been processed or accepted as correct. It only means HMRC received it.

Processing Timeline

Within 24-72 hours

HMRC's automated systems perform initial checks:

• Cross-referencing your figures against known data
• Checking for arithmetic errors
• Matching your UTR and company details

Within 1-2 weeks

Your return appears in your HMRC online account. You should see:

• The accounting period marked as "filed"
• Your tax calculation (if different from what you submitted)
• Any payment due or refund amount

Within 4-6 weeks (if refund due)

If your return shows a tax refund (e.g., you overpaid estimated payments), HMRC processes refunds within 4-6 weeks. The money goes to your company bank account on file with HMRC.

Checking Your Filing Status

Through Your Filing Software

Most CT600 software (including Taxpipe) shows the submission status:

• Submitted — sent to HMRC, awaiting acknowledgement
• Accepted — HMRC acknowledged receipt
• Rejected — HMRC returned an error (needs resubmission)

Through HMRC Online

Log into your HMRC business tax account:

1. Go to Corporation Tax
2. Select your company
3. View your accounting periods
4. Check the status of each period

What If HMRC Disagrees With Your Figures?

Discovery Assessment

If HMRC believes your return is incorrect, they can issue a discovery assessment to adjust your tax liability. This can happen up to 4 years after the end of the accounting period (6 years in cases of carelessness, 20 years for deliberate understatement).

Compliance Check (Enquiry)

HMRC may open a formal compliance check into your return. They must do this within 12 months of your filing date. If selected:

1. HMRC writes to you explaining what they want to check
2. They may request documents, records, or explanations
3. The enquiry concludes with either "no change" or an adjustment to your tax

Don't panic. Many compliance checks are routine. Respond promptly and honestly. If you used filing software, the software's records (audit trail, calculations) are valuable evidence.

Reasons HMRC Opens Enquiries

• Random selection (a percentage of all returns are checked)
• Figures that look unusual for your industry
• Large or sudden changes in turnover or profit
• Claims for significant reliefs (R&D credits, capital allowances)
• Information from third parties that doesn't match your return

Common Post-Filing Issues

"I filed but HMRC says I haven't"

This usually means:

• Your submission was rejected (check your software for error messages)
• You filed for the wrong accounting period
• There's a delay in HMRC's systems (give it 72 hours)

"HMRC says I owe more/less than I calculated"

HMRC performs its own calculation. Differences arise from:

• Rounding differences (usually trivial)
• Interest charges added to late payments
• Credits from previous periods being offset
• Errors in your calculation that HMRC corrected

"I need to change something"

You can amend your CT600 within 12 months of the filing deadline. Simply resubmit through your filing software.

Record Keeping After Filing

After filing, keep all supporting records for at least 6 years from the end of the accounting period:

• Bank statements and financial records
• Invoices and receipts
• Employment records
• Asset purchase documentation
• Board minutes and resolutions
• Your CT600 submission confirmation

HMRC can request these at any time during an enquiry.

Key Takeaways

File With Confidence

Taxpipe validates your CT600 before submission, minimising the risk of rejection. After filing, track your return's status directly in your Taxpipe dashboard.

File your CT600 → — £59, HMRC-validated, instant confirmation.

Related Reading

• Dormant Company CT600 Filing: Do You Still Need to File? (Yes — Here's How)
• HMRC Corporation Tax Refund: How Long?
• What Happens If You Don't File Corporation Tax? Penalties, Interest, and How to Fix It