This protocol presents a systematic approach for conducting exploratory modelling and analysis (EMA) to identify robust policy mixes for clean energy transitions. It explores the effects of diverse policy alternatives and multiple uncertainties within energy transitions through computational experiments. The protocol comprises diverse steps, including Decision Framing, Policy Alternatives Generation, Experiment Setting, Performing Experiments, Policy Alternatives Analysis, Performance Metrics Analysis, and Medium and Long-term Policy Analysis. It also integrates analytical sub-processes such as Policy Objectives Analysis, Feature Scoring, Robustness Analysis, Vulnerability Analysis, and Trade-off Analysis. The effectiveness of this protocol is demonstrated through its successful implementation in Mexico. Targeted at researchers, policymakers, and energy analysts, it offers a comprehensive method for in-depth exploration of the potential effects of diverse policy alternatives and multiple uncertainties within energy systems. While acknowledging that the duration of completion depends on available computational resources, it provides a detailed approach to conducting EMA for energy transitions.