The Paris Climate Agreement has motivated commercial organisations to set and work towards Science Based Targets, a realignment of greenhouse gas emissions in line with climate science. This work presents a modelling framework to develop cost-effective decarbonisation investment programs that address electricity and heat carbon emissions in organisations with multiple properties. The case study takes a set of 60 supermarkets in the UK and evaluates the techno-economic viability of installing biomethane combined heat and power engines and photovoltaic panels to make them zero carbon buildings. Simulation results from the batch of buildings offer the financial and environmental benefits at each site and generates a set of regression coefficients which are then applied into an optimisation problem. Solving the optimisation yields the decarbonisation investment strategy for the estate up to 2050; indicating the preferred sequence of investments the company needs to undertake to embark upon an effective low-carbon roadmap. A sensitivity analysis compliments the study to understand how market and policy externalities may influence roadmaps. Results suggest a CAPEX ranging from £57-£80 million is required to deliver an ambitious decarbonisation plan, while OPEX and carbon savings benefits range between £197 and £683 million and 461–715 ktCO2e; respectively. The case study highlights that although carbon targets can be achieved by 2030, the 2050 targets are more challenging to meet; suggesting additional technologies and policies should be considered and implemented. The framework serves as a blueprint of how modelling can assist decision-makers in reducing their carbon footprint cost-effectively to reach Science Based Targets.