Traditional nanofabrication techniques often require complex lithographic steps and the use of toxic chemicals. To move from the laboratory scale to large scales, nanofabrication should be carried out using alternative procedures that are simple, inexpensive and use non-toxic solvents. Recent efforts have focused on nanoimprinting and the use of organic resists (such as quantum dot-polymer hybrids, DNA and poly(ethylene glycol)), which still require, for the most part, noxious chemicals for processing. Significant advances have been achieved using 'green' resists that can be developed with water, but so far these approaches have suffered from low electron sensitivity, line edge roughness and scalability constraints. Here, we present the use of silk as a natural and biofunctional resist for electron-beam lithography. The process is entirely water-based, starting with the silk aqueous solution and ending with simple development of the exposed silk film in water. Because of its polymorphic crystalline structure, silk can be used either as a positive or negative resist through interactions with an electron beam. Moreover, silk can be easily modified, thereby enabling a variety of 'functional resists', including biologically active versions. As a proof of principle of the viability of all-water-based silk electron-beam lithography (EBL), we fabricate nanoscale photonic lattices using both neat silk and silk doped with quantum dots, green fluorescent proteins (GFPs) or horseradish peroxidase (HRP).