Deep decarbonisation – i.e. the transition towards net-zero emissions energy systems – will be enabled by a high penetration of intermittent renewables, storage and sector-coupling technologies. In this paper, we present a novel modelling approach to capture the increasing complexity of such future energy systems and help policy makers choose among the different possible transition scenarios. Salient features of our model, consisting of an extended and regionalised version of EnergyScope (Limpens et al., 2019 [1]), are a low computational time and a concise formulation which make it suitable for uncertainty and what-if analyses. As a case study, the model is applied to devise scenarios for the Italian energy transition. Specifically, we develop the first open-source whole-energy system model of Italy and assess the feasibility of its decarbonisation strategy with respect to uncertainties in the deployment of carbon capture and storage (CCS) and renewable technologies. Results show that emissions can be cut by 79%–97% vs. 1990 levels thanks to a radical electrification of the energy system coupled to a wide deployment of renewables and efficient energy conversion technologies. Finally, we discuss the synergies, advantages and disadvantages of our proposed approach with respect to alternative modelling approaches used across 88 recent deep decarbonisation studies. The analysis suggests that our model, thanks to its computational efficiency and a snapshot approach (i.e., modelling a target-year in the future), can complement more detailed and established energy models optimising the energy transition pathway (i.e., modelling the pathway from today to the target year).