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How can I verify Zerodha has passed the margin penalty I paid to the exchange?

The exchanges collect penalties from Zerodha for all clients and not client-wise. Hence, it’s not possible to share an acknowledgement from the exchange for the penalty you have paid.

The brokerage industry is one of the most heavily regulated industries. All Brokers are subject to multiple audits - both internal audits (done half-yearly) & external audits (carried out by the exchanges & SEBI). The scope of these audits includes carrying out checks that ensure a broker isn’t misusing clients funds, including charging a penalty and not passing it on to the exchange.

As brokers, we merely act as agents, collecting the penalty on non-upfront penalty and passing it on to the exchange.

You can check out these pages on NSE and MCX that explicitly mention the penalty rate for margin shortfalls.