Composting of biological waste constitutes an exothermic process. Some heat generated during composting is required to maintain the process and possible batch disinfection. The compost heap temperature increases often during the process up to 80ºC. According to the literature, the most advantageous composting temperature of the thermophilic phase is the temperature of 55ºC. However, excessive heat collection may be used at another location. Yet temperature inside the composting material shall not decrease below 50ºC as it may cause slowing down or even inhibition of the composting process. During composting, air supply (oxygen) is crucial to ensure optimum conditions for microorganism growth. Therefore the proper control of heat collection and airing process is required. The paper presents the fuzzy logic and LabView language based application that ensures control of the composting process. Conducted tests of the workstation and application confirmed heat collection of 101 MJ and pumping 0.68 m3 of water.