The paper describes a systematic framework that uses exergoeconomic theory integrated into ‘building energy retrofit’ (BER) design. An exergoeconomic module, based on the SPECO method, has been embedded into ‘EXRETOpt’, a recently developed retrofit-oriented exergy simulation tool based on EnergyPlus. Both active and passive technologies were analysed using two calibrated archetype non-domestic buildings as case studies (an office and a primary school). A novel cost-benefit indicator which accounts for building exergy destruction cost, retrofit annual capital cost, and project annual revenue is presented. This indicator is employed to account for best exergoeconomic performance technologies and to further develop deep BER packages. Compared to typical practice, exergoeconomics combined with cost-benefit provides a powerful tool for exploration and design improvement of building energy systems. In both cases, final product cost for heating and cooling processes were substantially reduced. In addition, the office case presented improvements in energy use by 67%, CO2 emissions by 53%, thermal comfort by 22%, exergy destructions by 42%, and the overall building exergy efficiency was improved from 14.8% to 20.0%. The school case presented similar results with an improvement of building exergy efficiency from 8.2% to 11.1%, and the potential to generate income due to current government incentives.