Nowadays, many organizations use Process Aware Information Systems (PAISs) to automate their business process. As any other information systems, security plays a major role in PAIS to provide a secure state and maintain the system in it. In order to provide security in a PAIS, a Process Aware Host-based Intrusion Detection (PAHID) model is proposed in this paper. The model detects host-based intrusions in a PAIS using process mining techniques. The proposed model uses both anomaly detection and misuse detection techniques for more efficiency, and organizational perspective of process mining is considered (rather than control-flow perspective) to detect more attack types. The model is automated and can deal with large logs and is suitable for flexible application domains. The PAHID model is implemented by the use of ProM framework and Java programming. It is evaluated by using a simulated log based on a real-world organization information system. Results demonstrate that the model provides high accuracy and low false positive rate.