Nanoparticle-polymer composites are important functional materials but structural control of their assembly is challenging. Owing to its crystalline internal structure and tunable nanoscale morphology, cellulose is promising polymer scaffold for templating such composite materials. Here, we show bottom-up synthesis of reducing end thiol-modified cellulose chains by iterative bi-enzymatic β-1,4-glycosylation of 1-thio-β-d-glucose (10 mM), to a degree of polymerization of ∼8 and in a yield of ∼41% on the donor substrate (α-d-glucose 1-phosphate, 100 mM). Synthetic cellulose oligomers self-assemble into highly ordered crystalline (cellulose allomorph II) material showing long (micrometers) and thin nanosheet-like morphologies, with thickness of 5–7 nm. Silver nanoparticles were attached selectively and well dispersed on the surface of the thiol-modified cellulose, in excellent yield (≥ 95%) and high loading efficiency (∼2.2 g silver/g thiol-cellulose). Examined against Escherichia coli and Staphylococcus aureus, surface-patterned nanoparticles show excellent biocidal activity. Bottom-up approach by chemical design to a functional cellulose nanocomposite is presented. Synthetic thiol-containing nanocellulose can expand the scope of top-down produced cellulose materials.