This paper addresses important links and synergies between two essential parts of an urban energy system, waste and transport sectors, respectively. Accomplishing sustainable urban development is a key challenge for cities addressing social equity, economic prosperity and the environment. Mobility needs in cities are continuously increasing and related emissions continue to affect air quality and contribute to climate change. At the same time, the amount of generated waste is also increasing. The aim of this paper is to develop a conceptual framework of waste-to-biomethane concept application in an urban energy system. A methodology for a techno-economic evaluation of biogas production and consumption is described with particular interest in biomethane application in the transport sector.