As the number of variants increases and customer requirements grow, factory planning becomes more relevant in a dynamic market environment. Development and expansion planning, in particular, significantly impact companies’ costs due to their high capital requirements and long lifetimes. Inaccurate estimates for the costs of factories can quickly lead to misinvestments and financial instability for companies. The interactions between factory configuration and the associated costs play a significant role in this context. Costs for planning projects must be estimated using a low-effort and reproducible procedure to avoid these misinvestments. With current methods and tools, this is not or only insufficiently possible. In preliminary work, requirements for cost estimation of factory planning projects have already been identified and prepared for a holistic approach. This article presents a methodological framework for a cost estimation approach. In a three-stage process, influences from an organizational perspective, the factory configuration and the related lifecycle-oriented cost estimation are considered. Considering different scenarios in the context of an outlook enables a final assessment of the opportunities and risks of different factory scenarios in the early planning phase.