A fast-paced policy context is characteristic of energy and climate research, which strives to develop solutions to wicked problems such as climate change. Funding agencies in the European Union recognize the importance of linking research and policy in climate and energy research. This calls for an increased understanding of how stakeholder engagement can effectively be used to co-design research questions that include stakeholders' concerns. This paper reviews the current literature on stakeholder engagement, from which we create a set of criteria. These are used to critically assess recent and relevant papers on stakeholder engagement in climate and energy projects. We obtained the papers from a scoping review of stakeholder engagement through workshops in EU climate and energy research. With insights from the literature and current EU climate and energy projects, we developed a workshop programme for stakeholder engagement. This programme was applied to the European Climate and Energy Modelling Forum project, aiming to co-design the most pressing and urgent research questions according to European stakeholders. The outcomes include 82 co-designed and ranked research questions for nine specific climate and energy research themes. Findings from the scoping review indicate that papers rarely define the term 'stakeholder'. Additionally, the concepts of co-creation, co-design, and co-production are used interchangeably and often without definition. We propose that workshop planners use stakeholder identification and selection methods from the broader stakeholder engagement literature.