Meso-structured onion-like silica (Meso-Onion-S) was synthesized and used as a host of enzyme immobilization. Meso-Onion-S has a 200-300 nm sized primary meso-structured onion building unit, and each onion unit has highly curved mesopores of 10 nm diameter in a multishell structure. Nanoscale enzyme reactors (NERs) in Meso-Onion-S were prepared via a two-step process of enzyme adsorption and subsequent enzyme cross-linking, which effectively prevents the leaching of cross-linked enzyme aggregates from highly curved mesopores of Meso-Onion-S. As a result, NERs in Meso-Onion-S significantly improved the enzyme stability as well as the enzyme loading. For example, NER of lipase (NER-LP) was stable under rigorous shaking for 40 days, while the control sample of adsorbed LP (ADS-LP) with no enzyme cross-linking showed a rapid inactivation due to rigorous enzyme leaching under shaking. Stable NER-LP was successfully employed to produce biodiesels and fatty acid methyl esters, from the LP-catalyzed transesterification of soybean oil with methanol. Interestingly, the specific activity of NER-LP was 23 and 10 times higher than those of free LP and ADS-LP, respectively, revealing the importance of LP stabilization in the form of NER-LP in the presence of organic solvents.