The recombinant lipase LipMatCCR11 from the thermophilic strain Geobacillus thermoleovorans CCR11 was applied in the synthesis of n-butyl caproate via transesterification in hexane and xylene. The short chain flavour ester was obtained by alcoholysis from ethyl caproate and n-butyl alcohol and acidolysis from n-butyl butyrate and caproic acid. This enzyme was also used in the condensation reaction from caproic acid and n-butanol. The conversion percentages at equilibrium (Xe) were similar to those obtained with Candida antarctica lipase fraction B (CAL-B) in the same reaction conditions, while lower conversion velocities (k) were attained. LipMatCCR11 reached high conversion percentages in either hexane or xylene as organic media (> 63%); the enzyme was also able to catalyze the aminolysis reaction of ethyl caproate with benzyl amine in hexane obtaining a conversion percentage > 62%.