Symbiotic relationships are ubiquitous on our planet, and a necessary component of life in all its forms. Symbioses have been identified in ecological contexts ranging from forests, to coral reefs, to the microbiota of humans. Despite their importance, the main body of theory largely neglects key features of host-symbiont relationships, such as their interdependent fitness and the fluctuating abundance of symbionts within a hosts’ lifetime. This lack of mathematical theory limits our predictive understanding of the ecological and evolutionary dynamics of these communities, and is affecting our ability to successfully manage and conserve them. During this workshop, biologists and mathematicians will come together to discuss the current challenges and opportunities for the mathematical modelling of symbiotic systems. Participants will develop the foundations of a new class of ‘eco-evolutionary’ models that explicitly accounts for host-symbiont intertwined ecology and evolution, and for the consequences of this interdependence. The developed models will help advance our mechanistic understanding of host-symbiont community dynamics, with implications ranging from forestry management, to coral reef conservation, to human health.