Described is an efficient stereocontrolled route into valuable, densely functionalized fluorinated phosphonates that takes advantage of (i) a Clostridial enzyme to set the absolute stereochemistry and (ii) a new [3,3]-sigmatropic rearrangement of the thiono-Claisen variety that is among the fastest sigmatropic rearrangements yet reported. Here, a pronounced rate enhancement is achieved by distal fluorination. This rearrangement is completely stereoretentive, parlaying the enzymatically established β-C–O stereochemistry in the substrate into the δ-C–S stereochemistry in the product. The final products are of interest to chemical biology, with a platform for Zn-aminopeptidase A inhibitors being constructed here. The enzyme, Clostridium acetobutylicum (CaADH), recently expressed by our group, reduces a spectrum of γ,δ-unsaturated β-keto-α,α-difluorophosphonate esters (93–99% ee; 10 examples). The resultant β-hydroxy-α,α-difluorophosphonates possess the “l”-stereochemistry, opposite to that previously observed for the CaADH-reduction of ω-keto carboxylate esters (“d”), indicating an unusual active site plasticity. For the thiono-Claisen rearrangement, a notable structure–reactivity relationship is observed. Measured rate constants vary by over 3 orders of magnitude, depending upon thiono-ester structure. Temperature-dependent kinetics reveal an unusually favorable entropy of activation (ΔS^‡ = 14.5 ± 0.6 e.u.). Most notably, a 400-fold rate enhancement is seen upon fluorination of the distal arene ring, arising from favorable enthalpic (ΔΔH^‡ = −2.3 kcal/mol) and entropic (ΔΔS^‡ = 4 e.u., i.e. 1.2 kcal/mol at rt) contributions. The unusual active site plasticity seen here is expected to drive structural biology studies on CaADH, while the exceptionally facile sigmatropic rearrangement is expected to drive computational studies to elucidate its underlying entropic and enthalpic basis.