GSTR-1 filed with all invoices for January, GST paid but GSTR-3B nil return filed

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Mostly they will be doing quarterly for saving tax consultancy fees.So you can make it happen on monthly basis.

@ CA Akshay Hiregang:

When a person files GSTR- 3B monthly and GSTR-1 monthly.Wont there be mismatch ??

Yes there would be a mismatch w.r.t vendors filing on quarterly basis. Therefore, reconciliation is to be maintained not only monthly basis but also on YTD (year to date basis). This will help ensure dynamic GSTR 2A report is considered, and even quarterly returns filers will be included. 

If department notice is received, you can share the reconciliation to prove vendors have filed the GSTR 2A is earlier months. Hope this clarifies. 

Considering the number of queries suggest you to get into a retainer to get quality and precise answers for your questions. 

Whether ITC reconciliation not apply on yearly basis.

First take ITC based on invoice and reconcile when the seller files GSTR-1

It is a combination of both now. You must have invoice (ITC to be eligible) + reflection in GSTR 2A. 

Suggest you to take written opinion if exposure if high.

Iam trying to post this query here so that atleast influencing people view this and do something for improvement

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