Nanoscale enzyme reactors (NERs) of glucose oxidase in conductive mesoporous carbons were prepared in a two-step process of enzyme adsorption and follow-up enzyme crosslinking. MSU-F-C, a mesoprous carbon, has a bottleneck pore structure with mesocellular pores of 26 nm connected with window mesopores of 17 nm. This structure enables the ship-in-a-bottle mechanism of NERs, which effectively prevents the crosslinked enzymes in mesocellular pores from leaching through the smaller window mesopores. This NER approach not only stabilized the enzyme but also expedited electron transfer between the enzyme and the conductive MSU-F-C by maintaining a short distance between them. In a comparative study with GOx that was simply adsorbed without crosslinking, the NER approach was proven to be effective in improving the sensitivity of glucose biosensors and the power density of biofuel cells. The power density of biofuel cells could be further improved by manipulating several factors, such as by adding a mediator, changing the order of adsorption and crosslinking, and inserting a gold mesh as an electron collector.