A compartment based inlet particle separator system for an aircraft that includes an auxiliary power unit (APU) system compartment is provided. The system includes a separation barrier wall, a ram air inlet opening, a diffuser, and an inlet particle separator (IPS). The separation barrier wall is disposed within the APU system compartment and divides the APU system compartment into two compartments. The ram air inlet opening is formed one of the compartments. The diffuser receives ram air from a ram air inlet opening and discharges ram air into a compartment. The IPS is disposed within the a compartment between the diffuser outlet and the APU air inlet port.