Aminoglycoside N-6′-acetyltransferases (AAC(6′)s) are important determinants of antibiotic resistance. A good mechanistic understanding of these enzymes is essential to overcome aminoglycoside resistance. We have previously reported the synthesis of amide-linked and sulfonamide-linked aminoglycoside-coenzyme A conjugates which were useful mechanistic and structural probes of AAC(6′)s. We report here the synthesis of a phosphonate-linked aminoglycoside-coenzyme A variant, which is expected to be a superior mimic of the tetrahedral intermediate proposed for catalysis by AAC(6′)s. This synthetic target is especially challenging for a number of reasons including the presence of multiple functional groups, the water solubility of both starting materials, and incompatibility of P(III) chemistry with water. We have overcome these challenges by adding the expensive coenzyme A in the last step via an elegant Michael-type addition onto a vinylphosphonate in water. Overall, a single protection step was needed. The decreased inhibitory potency of this bisubstrate compared to that of the amide-linked analog suggests that Enterococcus faecium AAC(6′)-Ii may not stabilize the proposed tetrahedral intermediate, and may act mainly via proximity catalysis.