Virtual design tools and methods can aid in creating decision bases, but it is a challenge to balance all the trade-offs between different disciplines in building design. Optimization methods are at hand, but the question is how to connect and coordinate the updating of the domain models of each discipline and centralize the product definition into one source instead of having several unconnected product definitions. Building information modelling (BIM) features the idea of centralizing the product definition to a BIM-model and creating interoperability between models from different domains and previous research reports on different applications in a number of fields within construction. Recent research features BIM-based optimization, but there is still a question of knowing how to design a BIM-based process using neutral file formats to enable multidisciplinary optimization of life-cycle energy and cost. This paper proposes a framework for neutral BIM-based multidisciplinary optimization. The framework consists of (1) a centralized master model, from which different discipline-specific domain models are generated and evaluated; and (2) an optimization algorithm controlling the optimization loop. Based on the proposed framework, a prototype was developed and used in a case study of a Swedish multifamily residential building to test the framework’s applicability in generating and optimizing multiple models based on the BIM-model. The prototype was developed to enhance the building’s sustainability performance by optimizing the trade-off between the building’s life-cycle energy (LCE) and life-cycle cost (LCC) when choosing material for the envelope. The results of the case study demonstrated the applicability of the framework and prototype in optimizing the trade-off between conflicting objectives, such as LCE and LCC, during the design process.