D-Allulose is considered an ideal alternative to sucrose and has shown tremendous application potential in many fields. Recently, most efforts on production of D-allulose have focused on in vitro enzyme-catalyzed epimerization of cheap hexoses. Here, we proposed an approach to efficiently produce D-allulose through fermentation using metabolically engineered Escherichia coli JM109 (DE3), in which a SecY (ΔP) channel and a D-allulose 3-epimerase (DPEase) were co-expressed, ensuring that D-fructose could be transported in its nonphosphorylated form and then converted into D-allulose by cells. Further deletion of f ruA, manXYZ, mak, galE, and f ruK and the use of Ni 2+ in a medium limited the carbon flux flowing into the byproduct-generating pathways and the Embden−Meyerhof−Parnas (EMP) pathway, achieving a ≈ 0.95 g/g yield of D-allulose on D-fructose using E. coli (DPEase, SecY [ΔP], ΔFruA, ΔManXYZ, ΔMak, ΔGalE, ΔFruK) and 8 μM Ni 2+ . In fed-batch fermentation, the titer of D-allulose reached ≈23.3 g/L.