The diffusion of renewable energy – particularly in transport – in cities may facilitate the transition away from fossil fuels, improve air quality and reduce greenhouse gas emissions. Past studies on this topic have focused on system modelling of diffusion pathways, technology characteristics and also estimations of future availability of renewable energy, whilst neglecting the agency of producers and users. This article assesses barriers to the diffusion of biogas for transportation in cities from a system and actor perspective. Using document studies and interviews in the cities of Basel, Switzerland, and Odense, Denmark, we identify the presence of conflicting political priorities and shifting strategic objectives, resulting in mixed signals concerning the role and viability of biogas for transportation. This underlines the importance of public sector support and coherent design and implementation of strategy and policy enabling the diffusion of renewable energy.