Whether naturally occurring or man-made, biological threats pose a severe risk in an increasingly globalized world. The dual-use nature of biological research, with its most recent advances in biotechnology (‘synthetic biology’, gene editing, nanotechnologies etc.) and the rapid diffusion of knowledge, raise proliferation concerns of biological weapons by non-state actors. Thus, there is an urgent need to develop measures intended to enhance diagnostic, prophylactic and therapeutic capabilities and capacities to improve the ability of society to combat infectious diseases outbreaks, as well as to alleviate the effects of bioterrorism attacks. We present here two examples of biotechnology usage for biodefence purposes: (i) plants as biofactories for the rapid production of improved biopharmaceuticals (‘Plant Molecular Farming’), and (ii) plant sequences as immune-modulating agents to enhance the efficacy of genetic vaccines. These platforms represent two promising (and complementary) approaches for the rapid and low-cost production of countermeasures (diagnostics and vaccine candidates) against emerging, re-emerging and bioterrorism-related infections. © 2018, Springer Science+Business Media B.V., part of Springer Nature.