This paper describes the bioreduction of four fluoroacetophenones with thermophilic bacteria (Bacillus sp. FPZSP005, B. subtilis FPZSP088, B. licheniformis FPZSP055 and BC-FPZSP051). The reduction reactions were performed under microwave irradiation and the thermophilic bacteria of the Bacillus genus provided moderate conversions to fluoroalcohols with yields in the 26-42% ranges and 5-62% e.e. When the reactions were carried out under conventional heating, they showed high conversions and selectivities (up to > 99% e.e.). This is the first study in the literature on the use of microwave irradiation with thermophilic bacteria applied on biocatalysis.