Upgradation of bio-based furans into chemicals and biofuels has received great interest recently. In this work, we reported selective synthesis of furan carboxylic acids from the corresponding aldehydes by recombinant Escherichia coli cells expressing 3-succinoylsemialdehyde-pyridine dehydrogenase (SAPDH) from Comamonas testosteroni SC1588. The effects of induction and reaction conditions on whole-cell catalytic oxidation of furfural (FF) were studied. High temperature induction resulted in decreased activities of recombinant cells, likely due to improper protein folding. Nonetheless, recombinant cells induced under high temperature enable the byproduct furfuryl alcohol to be faster re-oxidized into 2-furoic acid (FCA) than those induced under low temperature. So the yield and selectivity of FCA were improved significantly by using high temperature induction, at expense of slightly longer reaction periods. The activities of recombinant cells highly depended on pH. The tolerant levels of this recombinant strain toward FF and 5-hydroxymethylfurfural (HMF) were approximately 100 mM. FCA and 5-hydroxymethyl-2-furancarboxylic acid (HMFCA) were obtained with the yields of 95–98%. FCA of up to 147 mM was produced by a fed-batch strategy, in a quantitative yield. In addition, most aromatic aldehydes tested were transformed into the target carboxylic acids by this biocatalytic method, with the yields up to 100%.