How to File GSTR-9 With ClearTax GST Software?

Last Updated: August 1, 2025

GSTR-9 is one of the most elaborate GST filings that millions of businesses in India prepare for every year. It is not just another return, but a year-end summary that requires accuracy and keen attention to detail. However, as data is disseminated in different invoices, monthly returns, and ledgers, even experienced practitioners find themselves entangled in the nightmares of reconciliation.

Enter a smarter way to file: GST software by ClearTax. Designed to guide you through the clutter, it makes a boring task a guided, simplified one. Whether it is auto-fetching data or identifying mismatches before they become an issue, it strives to be accurate and fast. Let’s explore how to file GSTR-9 with ClearTax, and how ClearTax GSTR-9 reconciliation makes compliance effortless, shall we?

What is GSTR-9?

GSTR-9 is the annual return that every GST-registered taxpayer must file. It summarizes all outward supplies, inward supplies, tax paid, input tax credit availed, and other details for the entire financial year. The government uses this return to cross-verify data submitted in monthly or quarterly returns like GSTR-1, GSTR-3B, and GSTR-2A.

  • Filing GSTR-9 accurately is essential because…
  • It ensures compliance and avoids penalties.
  • It helps reconcile your books with GST returns.
  • It provides a complete picture of your tax liability and credits.
  • It is mandatory for all regular taxpayers except for a few categories, like composition dealers.

Given the volume of data and complexity, manual filing can be prone to errors. This is why many businesses prefer using ClearTax GST for GSTR-9 filing.

Suggested Read: What is GSTR-9? Annual Return Filing Explained

How to File GSTR-9 With ClearTax GST Software?

Wondering how to file GSTR-9 with ClearTax? Well, here’s a step-by-step guide to help you file GSTR-9 in the most efficient possible manner…

Step 1: Register and log in to your account on the ClearTax GST software. If you are a first-time user, please create an account by filling in your details before going ahead with the filing process.

Step 2: Enter your GSTIN to link your business profile with ClearTax. The software also supports the use of multiple GSTINs, which is convenient for businesses with multiple registrations.

Step 3: ClearTax GST software automatically downloads your GSTR-1, GSTR-2A, and GSTR-3B data from the GST portal. You can also upload your books of accounts for reconciliation purposes.

Step 4: Use the ClearTax Assistant tool to initiate the filing. It helps with secure login to the GST portal and ensures smooth data fetching.

Step 5: Compare your sales and purchase data in returns and accounting books with the help of the ClearTax GSTR-9 reconciliation tool.

ClearTax GST

4.0

Starting Price

Price on Request

Step 6: Review the Observation tab, which highlights issues like missing HSN codes, mismatched liabilities, or ITC claims. This acts as a checklist to fix errors before final submission.

Step 7: Prepare the HSN Summary for outward and inward supplies using ClearTax’s built-in tool. This is a mandatory part of the GSTR-9 form.

Step 8: Add working notes if needed. These notes help explain adjustments and are useful for audits or future reference.

Step 9: ClearTax auto-fills most sections of the GSTR-9 form with reconciled data. It is still possible to manually review and edit any section in case it is necessary.

Note: ClearTax also has a complete ClearTax GSTR-9 tutorial built into the site. The tutorial takes you through all the parts of the form, the information you need to fill in, and the pitfalls to watch out for. It also gives checklists to make sure that your data is good to go before submitting.

ClearTax GST

4.0

Starting Price

Price on Request

Step 10: Download the finalized GSTR-9 JSON file from ClearTax.

Step 11: Log in to the GST portal, go to Annual Return, and upload the JSON file under Prepare Offline.

Step 12: File it using a Digital Signature Certificate (DSC) or Electronic Verification Code (EVC).

Step 13: Once the filing is successful, download the acknowledgment receipt.

Why Should You Choose ClearTax GST Software for GSTR-9 Filing?

Many businesses prefer ClearTax GSTR-9 filing because of the following benefits…

  • Automation Saves Time: ClearTax automates the whole process of downloading and filing data. You do not have to enter the data manually or access the GST portal regularly. This saves time.
  • Manage Multiple GSTINs Easily: If your business is registered under multiple GSTINs, ClearTax helps you file returns for all of them using a single dashboard.
  • Accurate ClearTax GSTR-9 Reconciliation: ClearTax GSTR-9 reconciliation is one of the software’s most effective capabilities. It checks your returns against your books and GST portal to identify mismatches (if there are any) at an earlier stage. This minimises the chances of mistakes and subsequent penalties.
  • User-Friendly Interface & Tutorials: ClearTax comes equipped with an easy-to-use interface along with a ClearTax GSTR-9 tutorial, so even those filing for the first time can do so without any qualms.
  • Quick Filing Option: For small businesses primarily, ClearTax offers a ‘Quick GSTR-9’ filing option that finishes the process in less than 10 minutes.
  • Secure & Cloud-Based: ClearTax GST software is a cloud-based program. Owing to this, your data remains safe, backed up, and accessible anytime, anywhere.
  • Expert Support: ClearTax has a dedicated customer support team to assist you with any questions or issues arising during the filing process.

Conclusion

Filing your GSTR-9 annual return on ClearTax makes the process less complex and time-consuming. With help from ClearTax GSTR-9 tutorial and automation functionality, importing data and reconciling it further has become easier than ever before.

Whether you manage a single GSTIN or loads of them at a time, ClearTax simplifies GSTR-9 filing, helping you avoid errors and stay compliant effortlessly. What are you waiting for them? Contact Techjockey and get your hands on the tool today!

Published On: August 1, 2025
Yashika Aneja

Yashika Aneja is a Senior Content Writer at Techjockey, with over 5 years of experience in content creation and management. From writing about normal everyday affairs to profound fact-based stories on wide-ranging themes, including environment, technology, education, politics, social media, travel, lifestyle so on and so forth, she has, as part of her professional journey so far, shown acute proficiency in almost all sorts of genres/formats/styles of writing. With perpetual curiosity and enthusiasm to delve into the new and the uncharted, she is thusly always at the top of her lexical game, one priceless word at a time.

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