How to File GSTR-6 Using ClearTax?

As companies grow in size, most central teams have access to input services in the name of the branches they represent and claim the Input Tax Credit (ITC) accordingly.

This is processed using the Input Service Distributor (ISD) mechanism in GST.

To maintain transparency and compliance, ISDs must submit GSTR-6, a monthly return displaying the information on ITC claimed and given. As an ISD that wants to file GSTR-6 easily in an automated manner, ClearTax is a smart way out.

This blog takes you through all the information about GSTR-6 and how to file GSTR-6 using ClearTax in a step-by-step process.

What is GSTR-6?

GSTR-6 is a monthly return that should be lodged by each Input Service Distributor. It records the position of input tax credit earned on inward supplies of services and the way this credit is fragmented to the entitled branches or units in India. The returns are comprehensive, including invoice-level data and corrections.

Suggested Read: Step-by-Step Guide on How to File GSTR-6 Online

Why is GSTR-6 Important?

GSTR-6 makes sure that the ITC availed by the head office or central team is passed to the qualified receivers properly. Without this return:

• Branches may miss out on eligible credit
• The risk of credit mismatches increases
• Businesses may face non-compliance penalties

You have to file GSTR-6 even when it is a nil return. Further, due to recent changes in the law, the ISD mechanism has become compulsory with effect w.e.f 1st April 2025. And thus, it is more important than ever that all filings should be done in time and accurately.

When is GSTR-6 Due?

The filing date of GSTR-6 is the 13th of the next month of the tax period. As an example, June 2025 returns should be filed by 13th July 2025.

When it comes to late filing, it carries a penalty of INR 50 per day. This is, however, true even in a case of nil returns.

Latest Legal Updates

• The ISD mechanism has now become mandatory by Notification No. 16/2024 (dated 6th August 2024) as an amendment to Section 2(61), Section 20 of the CGST Act.
• Notification No. 12/2024 (dated 10th July 2024) amended Rule 39 of the CGST Rules to specify the procedure of the ITC distribution, which, however, is yet to be notified.
• July 2025 also has a new restriction that a GSTR-3B cannot be filed beyond three years of its due date.

Detailed Breakdown of GSTR-6 Sections

The GSTR-6 return contains 11 key sections, covering GSTIN, credit received, distribution, mismatches, and more. These include:

1. GSTIN and Name – Auto-filled.
2. ITC Received for Distribution – Invoice-level credit details.
3. Total/Eligible/Ineligible ITC – Segregated ITC summary.
4. Distribution of ITC – Allocation to various GSTINs.
5. Amendments – Edits to previously filed data.
6. Mismatch and Reclaims – Adjustments for mismatches.
7. Redistribution – Corrections of wrongly distributed ITC.
8. Late Fees and Refunds – Amounts paid and claimed.

Now that we’ve understood the structure and importance of GSTR-6, it is time to move to the most important part of this blog, which is how to file GSTR-6 using ClearTax..

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How to File GSTR-6 Online Using ClearTax?

You can file GSTR-6 through the GST portal or any GST software. As of now, we are using ClearTax, which has an easy-to-use dashboard through which businesses can upload, validate, reconcile, and file GSTR-6. It’s not necessary to log in to the government portal at each phase. Here’s a complete guide:

Prerequisites Before Filing GSTR-6 using ClearTax: File GSTR-6 Online Using ClearTax

• Ensure you’ve prepared the GSTR-6 data in an Excel format compatible with ClearTax’s template.
• Keep login credentials to the GST portal handy for final submission.
• Make sure invoice-level details are accurate to avoid reconciliation issues later.

Step-by-Step Process to File GSTR-6 using ClearTax

Step 1: Log in to ClearTax GST Dashboard

• Go to ClearTax and log in to your account.
• On the dashboard, click on ‘File GST Returns’.

Step 2: Choose Your Business Entity

• Under ‘Choose a Business’, search and select the business entity acting as the Input Service Distributor (ISD).
• Click on the ‘ISD Monthly’ option to proceed.

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Step 3: Select the Tax Period

• From the drop-down menu, choose the relevant month (e.g., June 2025).
• Click on the ‘Prepare GSTR-6’ tile to begin filing.

Step 4: Import Your GSTR-6 Data

• Click on ‘Import Documents’.
• Select ‘Government Excel’ as the import method.
• Upload your prepared Excel file by clicking ‘Select file from your computer’.
• Wait for the system to process and import your data.
• Once imported, a confirmation message appears showing the number of documents and sheets processed. Click ‘Proceed’ to continue.

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Step 5: Fix Any Errors in Your Data

• If there are any data errors, they’ll be shown in a tab.
• You can choose to:
  a) Fix errors immediately by editing rows and clicking ‘Save and Validate’, or
  b) Download errors in Excel, fix offline, and re-upload the corrected file.
• Alternatively, you may skip fixing by clicking ‘Continue without Fixing’ (though not recommended).

Step 6: Finalize Your Data & Reconcile

• After validation, click on ‘Proceed’ to prepare the GSTR-6 form.
• You can now preview details under various sections like Table 3, Table 4, etc.
• Use the ‘Total ITC Available & Eligible/Ineligible ITC’ option to auto-generate reconciliation tables.
• This is especially useful when reconciling credits claimed by branches vs. credits received.

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Step 7: Upload Data to GST Portal

• Once reviewed, click on ‘Save to GSTN Portal’.
• Enter your GST portal login credentials, fill in the CAPTCHA, and click ‘Submit’.
• If the upload fails, click ‘Retry’ to attempt again.
• Errors encountered will be highlighted, and you’ll get an Excel report to fix them.

Step 8: Final Filing on GST Portal

• On successful upload, a message will say ‘Your returns are ready to be filed!’
• Follow the prompt to complete the final submission on the official GST Portal.
• You can preview, edit, or delete invoices directly on ClearTax as well if needed.

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Additional Features from ClearTax

• Smart Reconciliation: Automatically brings to attention mismatches between the supplier and ISD data.
• Downloadable Reports: Print out reports in a tabular form in order to conduct an audit and record keeping.
• Error Assistance: Errors are more readily corrected due to detailed feedback.
• Auto-fill Tables: Eliminates manual typing and speeds up filing time by 50 percent or more.

Conclusion

The GSTR 6 may appear overwhelming because it is invoice-level and requires many reconciliation points. But with ClearTax GST software, Input Service Distributors can automate the entire process, upload the data, and finally submit without much manual processing and with maximum precision.

With thousands of invoices or multiple branches, ClearTax helps you get your GSTR-6 return right on time without any errors or delays.

Remain compliant and stress-free! File your GSTR-6 using ClearTax today.