A method is developed for encapsulation of bacterial biocatalysts in silica gels formed by silica nanoparticles (SNP) and a silicon alkoxide crosslinker. Formulation of the gel was optimized by changing the SNP size, SNP to crosslinker ratio and crosslinker functionality. Hydrolysis and condensation reactions of silicon alkoxide were controlled by water to alkoxide ratio (r) and pH of the solution. FTIR analysis verified that a reactive and temporally stable silicon alkoxide crosslinker was obtained. As a case study, recombinant Escherichia coli (E. coli) cells expressing the atrazine dechlorinating enzyme AtzA were encapsulated. Synthesized catalytic biomaterials (silica gel encapsulated bacterial biocatalysts) were evaluated based on their gelation time, biocatalytic activity and mechanical strength. Diffusivity assays and SEM were used for characterization of the gel structure. We found that SNP to crosslinker ratio affected all the features of the gel, whereas crosslinker functionality primarily affected the gelation time and SNP size affected the mechanical strength and diffusivity. Based on systematic evaluation, we selected three gel formulations and subjected them to long-term activity measurements in a continuous-flow bioreactor for removing trace levels of atrazine. The effluent atrazine concentration was sustained below 30% of the influent concentration, <3 ppb, for 2 months.