Smallholder farmers and manufacturers in the Agri-Food sector face substantial challenges because of increasing circulation of counterfeit products (e.g., seeds), for which current countermeasures are implemented mainly at the secondary packaging level, and are generally vulnerable because of limited security guarantees. Here, by integrating biopolymer design with physical unclonable functions (PUFs), we propose a cryptographic protocol for seed authentication using biodegradable and miniaturized PUF tags made of silk microparticles. By simply drop casting a mixture of variant silk microparticles on a seed surface, tamper-evident PUF tags can be seamlessly fabricated on a variety of seeds, where the unclonability comes from the stochastic assembly of spectrally and visually distinct silk microparticles in the tag. Unique, reproducible, and unpredictable PUF codes are generated from both Raman mapping and microscopy imaging of the silk tags. Together, the proposed technology offers a highly secure solution for anticounterfeiting and product traceability in agriculture.