Due to the popularity of the Near Field Communication (NFC) applications, NFC technology is being adopted by a wide variety of devices suitable for the Internet of things (IoT). However, NFC is vulnerable to numerous networking attacks such as tag manipulation. In this paper, a security-aware architecture is introduced to protect the NFC devices and associated data from several attacks. The proposed NFC system has a secure protocol, connected to the NFC chip. The NFC Data Exchange Format (NDEF) message is enriched with a certificate record. The proposed NFC system checks the authenticity of the sender first; then if appropriate, processes the incoming NDEF messages and stores them in device memory. The proposed NFC system is simulated using MATLAB. Simulation results suggest that the proposed protocol offers better security by detecting certificate modification, message modification, etc. It is also observed that the processing time remains almost the same for various record sizes and the processing time slightly increases as the certificate size increases. Therefore, the proposed NFC architecture has potential to be used in IoT devices.