Urban systems account for about two-thirds of global primary energy consumption and energy-related greenhouse gas emissions, with a projected increasing trend. Deep geothermal energy and woody biomass can be used for the production of heat, electricity and biofuels, thus constituting a renewable alternative to fossil fuels for all end-uses in cities: heating, cooling, electricity and mobility. This paper presents a methodology to assess the potential for integrating deep geothermal energy and woody biomass in an urban energy system. The city is modeled in its entirety as a multiperiod optimization problem with the total annual cost as an objective, assessing as well the environmental impact with a Life Cycle Assessment approach. For geothermal energy, deep aquifers and Enhanced Geothermal Systems are considered for stand-alone production of heat and electricity, and for cogeneration. For biomass, besides direct combustion and cogeneration, conversion to biofuels by a set of alternative processes (pyrolysis, Fischer-Tropsch synthesis and synthetic natural gas production) is studied. With a scenario-based approach, all pathways are first individually evaluated. Secondly, all possible combinations between geothermal and biomass options are systematically compared, taking into account the possibility of hybrid systems. Results show that integrating these two resources generates configurations featuring both lower costs and environmental impacts. In particular, synergies are found in innovative hybrid systems using excess geothermal heat to increase the efficiency of biomass conversion processes. The application to a case study demonstrates the advantages of using a system approach for the analysis over a stand-alone comparison between options.