Methods and systems for using physical payment cards in secure e-commerce transactions

Methods and systems for conducting a secure online transaction with a physical payment card. In an embodiment, a user computer identifies, during an online transaction, a selection of a secure payment option involving a physical payment card. Next, a security module of the user computer enters a secure transaction mode of operation which prevents other applications running on the user computer from access to cardholder data, establishes a communication session with a payment provider device, and prompts a user to present a payment card to a card reader device associated with the user computer. The card reader device then reads cardholder data from the physical payment card, and the security module creates a request message. The security module then transmits the request message to a payment provider computer (which provides substitute payment card details to the merchant computer to complete the online payment transaction) and exits the secure transaction mode.