This paper reports the use of an array of calorimetric micro-sensors that perform bidirectional measurement of wall shear stress, for flow separation detection and control. The sensors design is hot-wire like with three parallel micro wires suspended over a micro-cavity and mechanically supported using periodic perpendicular micro-bridges. The micro-sensors were implemented on a flexible packaging and characterized in a turbulent boundary layer wind tunnel on a flat plate. An array of twelve micro-sensors were then implemented in a flap model designed for active flow control experiments and equipped with pulsed jet actuators. The work included the design and manufacturing of appropriate miniaturized electronics. Without control, the micro-sensors successfully detected the natural flow separation and the flow separation point moving from the trailing edge to the leading edge as the angle of the flap increased. Finally, the micro-sensors characterized the efficiency of the active flow control for avoiding separation.