Glucosinolates (GSLs) are nitrogen- and sulfur-containing metabolites that contribute to human health and plant defense. The biological activities of these molecules are largely dependent on modification of the GSL R-groups derived from their corresponding amino acid precursors. In Arabidopsis seeds, esterification of the R-group of hydroxylated GSLs (OH-GSLs) leads to the accumulation of benzoylated GSLs (BzGSLs) and sinapoylated GSLs (SnGSLs). BzGSLs were thought to be synthesized from OH-GSLs and benzoyl CoA by a BAHD acyltransferase, but no BAHD gene is strongly co-expressed with the two reference genes BZO1 and AOP3 that are required for BzGSL biosynthesis. In contrast, three genes encoding serine carboxypeptidase-like (SCPL) acyltransferases [SCPL5, SCPL17 and SCPL19 (SNG2)] do exhibit strong co-expression. Using a reverse genetic approach, we found that the GSL profile of the scpl5 mutant was identical to that of wild-type, but both BzGSLs and SnGSLs were barely detectable in scpl17 mutants and their amounts were decreased in the sng2 mutant. In addition, both scpl17 and sng2 mutants accumulate the putative BzGSL precursors OH-GSLs and benzoylglucose. The results of further GSL analyses in other phenylpropanoid mutants and benzoate feeding experiments suggested that SCPL17 mediates the acyltransferase reaction directly, while the mutation in sng2 causes a decrease in BzGSLs and SnGSLs via an unknown indirect mechanism. Finally, benzoate feeding experiments using bzo1 mutants and BZO1 biochemical characterization indicated that the in vivo role of BZO1 is to synthesize the benzoate precursor cinnamoyl CoA rather than to generate benzoyl CoA from benzoate and CoA as previously predicted.