The invention relates to an enzymatic acylation method including at least the following steps of: contacting at least one compound having at least one function selected from among the amine, alcohol, or thiol functions, at least one microorganism having an acyl transfer activity and/or an acyl transfer enzyme, and at least one acylphosphonate donor of formula (I), where: R is an alkyl, alkene, alkyne, aryl, or aralkyl radical, or is —ORa, —SRa, —NRaRb, where Ra and Rb are identical or different and are H, an alkyl, alkene, alkyne, aryl or aralkyl radical, the alkyl, alkene, alkyne, aryl or aralkyl radicals being optionally substituted; X is O or S; Y and Z, which are identical or different, are —OR1, —OR2, —SR1, —SR2, —NR′1R″1, —NR′2R″2; R1, R2, R′1, R′2, R″1 and R″2, which are identical or different, are an alkyl, alkene, alkyne, aryl or aralkyl radical, said alkyl, alkene, alkyne, aryl or aralkyl radicals being optionally substituted; and recovering the compound including at least one acyl function, said function being selected from among the amine, alcohol, or thiol functions.