Example methods are provided for secure communication protocol processing in a network environment. The method may comprise, in response to detecting a first transport protocol packet that is addressed from a first endpoint to a second endpoint and includes unencrypted payload data and a first sequence number, generating and sending a first secure communication protocol packet that includes encrypted payload data and a second sequence number. The method may also comprise, in response detecting a second transport protocol packet that includes the first sequence number, determining that the second transport protocol packet is a retransmission of the first transport protocol packet. The method may further comprise generating and sending a second secure communication protocol packet that includes the second sequence number associated with the first sequence number.