The aims of this study are immobilization of formaldehyde dehydrogenase (FDH) into nano-space of nanostructured carbon and evaluation as a possible sensor detecting low concentration formaldehyde. In order to understand the effect of carbon pore size on activity and stability of FDH, mesoporous carbon (MC), originally made in our lab, and commercially available ketjen black (KB) were used in this study. Enzyme activity and electrochemical sensing ability of FDH encapsulated into such two carbon materials were compared. Our original MC resulted in favourable in some evaluated conditions but not in other conditions. MC adsorbed FDH less than KB, but enzyme activity was higher on MC per FDH. Stability against methanol increased on MC, but stability against water was rather lower on MC. Electrochemical sensing ability toward formaldehyde resulted in much better on KB, which was able to detect the sub-ppb level of formaldehyde. Consequently, such dependence is resulted by available nano-space of carbon, and so tuning the pore size of carbon is an important factor in order to develop enzyme based electrochemical sensors with high sensitivity and stability.