Monoterpenoid indole alkaloids (MIA) are a diverse class of secondary metabolites important for plant protection and are drugs for treating human diseases. Arabidopsis thaliana (L.) is not known to produce MIAs, yet its genome has 15 genes with similarity to the periwinkle (Catharanthus roseus (L.) G. Don) strictosidine synthase (STR) gene. Phylogenetic analysis of strictosidine synthase-like (SSL) proteins reveals four well supported classes of SSLs in Arabidopsis. To determine if Arabidopsis produces active strictosidine synthase, Arabidopsis protein extracts were assayed for enzymatic activity and cDNAs were expressed in Escherichia coli. Arabidopsis protein extracts from leaves and hairy roots do not make strictosidine at levels comparable to C. roseus, but they metabolise one substrate, secologanin, a precursor of strictosidine in other plant species, and produce an ‘unknown’ compound proposed to be a dimer of secologanic acid. Recombinant Arabidopsis proteins expressed in E. coli were not active STRs. Quantitative PCR analysis was performed on class A Ssls and showed they are upregulated by salt, ultraviolet light and salicylic acid treatment. RNAi mutants of Arabidopsis with reduced expression of all four class A Ssls, suggest that class A SSL proteins can modify secologanin. Gene expression and metabolomics data suggests that class A Ssl genes may have a role in plant protection.