A method for preventing a message from being modified or deleted by a malicious application when the message is received by an electronic device based on a service provided in the electronic device and an electronic device therefor are provided. The method includes successively loading at least two received messages in a sequence filter, and determining whether data of the at least two received messages are identical to each other. A method for operating an electronic device is not limited to the above method, and other embodiments are possible within the same or similar scope as the present disclosure.