As part of Zerodha's risk management measure, the margin is updated after reducing 0.3% + applicable PIS reporting charges from the total PIS account balance shared by the banks. This is done to avoid delays in settlement from the bank due to insufficient funds in the PIS account.

If the purchase price of the shares is less than the margins updated in the Zerodha account, the available margin in the PIS account is reduced by the purchase price and is then updated in the Zerodha account the next day.

Example scenario

• Funds in the PIS account is ₹10,00,000. The margin in the Zerodha account would be approximately ₹9,97,000 ( ₹10,00,000 * 99.7%). If shares worth ₹9,96,000 were purchased and the charge for it was ₹2,900. A contract note is sent to the bank for ₹9,98,900. This gets settled by the bank as there is sufficient balance in the PIS account, i.e. ₹10,00,000.
  
  
• Funds in the PIS account is ₹10,00,000. The margin in the Zerodha account would be approximately ₹9,97,000 ( ₹10,00,000 * 99.7%). If shares worth ₹1,00,000 were purchased, the charge for it was ₹310. A contract note would be sent to the bank for ₹1,00,310. This gets settled by the bank as there is sufficient balance in the PIS account, and the balance in the PIS account would be ₹8,99,690 (₹10,00,000 - ₹1,00,310). The margin updated the next day in the Zerodha account would be ₹8,96,990.93 (₹8,99,690 * 99.7%).