Despite the excitement around the nexus between land, energy and water resource systems, policies enacted to govern and use these resources are still formulated in isolation, without considering the interdependencies. Using a Ugandan case study, we highlight the impact that one policy change in the energy system will have on other resource systems. We focus on deforestation, long term electricity supply planning, crop production, water consumption, land-use change and climate impacting greenhouse gas (GHG) trajectories. In this study, an open-source integrated modelling framework is used to map the ripple effects of a policy change related to reducing biomass consumption. We find that, despite the reduction in deforestation of woodlands and forests, the GHG emissions in the power sector are expected to increase in between 2040–2050, owing to higher fossil fuel usage. This policy change is also likely to increase the cost of electricity generation, which in turn affects the agricultural land types. There is an unforeseen shift from irrigated to rainfed type land due to higher electricity costs. With this integrated model setup for Uganda, we highlight the need for integrated policy planning that takes into consideration the interlinkages between the resource systems and cross propagation effects.