Avalara > Blog > Goods and Services Tax > Demystifying GSTR-9 — Part 2 How to file Annual GST Return and make tax payments

Demystifying GSTR-9 — Part 2: How to file Annual GST Return and make tax payments

  • Feb 7, 2019 | CA Priya Madrecha (CA,CS)

Note: The due date to file annual GST return form GSTR-9 for FY 2018-18 has been further extended to November 30, 2019.

In our series of two articles, we are attempting to shed light on everything taxpayers need to know about the annual GST return, GSTR-9. 

Part 1 of this series examined the basics of the GSTR-9 return form, including its format. 

In this article, Part 2, we are looking at procedures for filing GSTR-9 returns, as well as potential penalties.

How to file GSTR-9?

The Central Board of Indirect Taxes and Customs (CBIC) issued instructions for filing both GSTR-9 and GSTR 9A returns, as well as GSTR-9C, the Annual Reconciliation Statement, in September 2018. As with other GST return forms, taxpayers may file the annual GSTR-9 directly online on the GST Common Portal. Taxpayers may also file offline by downloading an excel template, and then uploading it to the GST Portal.


  • Taxpayers can download a system-computed GSTR-9 return in PDF format. Values in each table of GSTR-9 will be auto-populated to the extent possible based on figures from GSTR-1 and GSTR-3B returns filed during the previous year. 
  • Taxpayers may access consolidated summaries of previously filed GSTR-1 and GSTR-3B returns as PDFs. 
  • A Taxpayer will be able to edit the values within those previously filed return with some exceptions, including values in table 6A, 8A, as well as tax payment entries in table 9. 
  • A 'Nil' return can be filed with a single click. 


  • Taxpayers may download an offline tool from the portal. 
  • An auto-populated GSTR-9 should be downloaded from the portal before filling in remaining values. 
  • Values in table 6A, table 8A, as well as tax payment entries in table 9, will be non-editable. 
  • After filling in the remaining values, taxpayers will generate and save a JSON file.  
  • After logging on the portal, taxpayers will upload the JSON file. 
  • The JSON file will be processed and any errors will be shown. 
  • Because there is no facility for revising JSON files online, taxpayers should download any files with errors from the portal and open them in the Excel tool. 
  • After making corrections and reconciling information in the return and in the books, taxpayers should upload and refile the return via the portal. 
  • Corrections can be made in case of online data entry of invoices, except table 17 & 18 if the number of records exceeds 500 in each table. 
  • After filing, returns can be downloaded as either PDFs or Excel files. 

However, the facility to file this form has not been enabled yet on the portal.

Payment of additional liability

Any additional liability based on errors previously missed should be reported in either the GSTR-1 or GSTR-3B returns that pertain to financial year 2017-18. The same errors will be reported in subsequent GSTR-1 or GSTR-3B returns up to September 2018. However, if the previously missed errors should be reported in GSTR 1 or GSTR 3B up to September 2018, the government has not provided clarity on whether the additional liability can be paid through GSTR 3B or DRC-03. Late fees can be paid along with GSTR 9 returns, however.

Penalties for delays in furnishing annual returns

Section 47 of the GST act deals with penalties for delays in furnishing annual returns. Failure to file annual returns on time shall attract a late fee of INR 200 per day (INR 100 for CGST and INR  100 for SGST; there is no late fee for IGST) during the period of failure, subject to a maximum of 0.25% of the applicable financial year's turnover.


One important aspect to keep in mind is that the GSTR-9 return allows taxpayers to provide only information that has already been furnished in previous monthly or quarterly returns. No new information can be added, and no errors may be corrected. In a layman’s language, GSTR-9 is an aggregation return. This has led to some contention in the industry, as many taxpayers hoped to be able to rectify errors committed in previous GSTR 3B & GSTR 1 returns during the process of preparing the GSTR-9 annual return.

GST Council finalized the contents of the GSTR-9 annual return with the dual goals of achieving simplicity and comprehensiveness, but many believe it hasn’t yet achieved either. Many taxpayers remain confused about the forms numerous requirements. Industry’s primary demand had been for the Council to do away with the requirement to segregate inputs, input services, and capital goods, however, thus far, the Council has rejected this demand.

Taxpayers are likely to find that the new GSTR-9 return filing process involves its own share of challenges. Time will tell how the industry copes with GSTR-9’s additional compliance burdens, however, many businesses will find using GST compliance software can greatly assist them in filing GST annual returns smoothly and accurately.

Avalara is an experienced application service provider (ASP) and partner of authorized GST Suvidha Providers (GSPs). To understand how our cloud-based application Avalara India GST can help you with GST compliance automation, contact us through https://www.avalara.com/in/products/gst-returns-filing.

Avalara helps businesses of all sizes get GST return filing, e-way bill generation and e-invoicing right with cloud-based GST compliance solutions in India. Goods and Services Tax (GST) rates, rules, and regulations change frequently. Although we hope you'll find this information helpful, this blog is for informational purposes only and does not provide legal or tax advice.
Avalara Author
CA Priya Madrecha (CA,CS)
Avalara Author CA Priya Madrecha (CA,CS)
Priya is a Chartered Accountant by profession and also a qualified Company Secretary. She is a Partner at Madrecha & Co. in Mumbai. She is a moderator for gstindia.net, a forum on Goods and Services Tax. An ex-consultant at KPMG, she specializes in taxation. Priya is an avid reader and has a flair for writing.