The actual paper presents an embedded flight control systems (EFCS) of two micro air vehicles (MAVs) concepts, the gun-launched MAV (GLMAV) and the aircraft-launched MAV (ALMAV), meant to rapidly reach a target zone further away from the launching point. The paper details the embedded architecture used by both vehicles at software and hardware level. The software layer contains the algorithms to process the onboard sensors information as well as to compute the control law. The hardware layer features the bidirectional communication link with the ground workstation and interfaces the control commands with the actuators. The key element of the overall embedded processing architecture is the Gumstix-COM which operates under the Xenomai real-time framework. Concerning the configuration of the airframe, we provide a descriptive study of the transition phase, covering the dynamic model and control scheme. The evaluation of the two concepts implies a comparative, regarding to identify similarities and differences of the configuration, i.e. advantages and drawbacks. Motivating simulations results were obtained in the evaluation of the flight controller within the transition phase. The experimental evaluation of the proposed EFCS during autonomous attitude-stabilized flight has returned promising results.