This paper delves into the integration of Factories of the Future (FoF) and digital twin technologies within urban contexts, marking a significant leap in Smart Cities development. We present a thorough exploration of the principles and a scientifically grounded framework designed for seamlessly blending advanced manufacturing systems with the urban environment’s digital and physical aspects. Our detailed analysis has identified core principles crucial for this integration, focusing on interoperability, sustainability, adaptability, stakeholder collaboration, and strong data governance. We propose a structured framework that puts these principles into action, outlining strategic routes for incorporating digital twin and Building Information Modeling (BIM) technologies into FoF, establishing public-private partnerships, enhancing education and workforce development, and setting up mechanisms for ongoing evaluation and enhancement. The potential of this integration to transform urban development is vast, providing a model for boosting operational efficiency, driving economic growth, and enhancing urban livability. Although challenges exist in realizing this vision, our research offers practical insights and strategies for cities and industries to effectively navigate the complexities of the digital era. This contribution enriches the growing field of urban science, advocating for a harmonious integration of industrial production with urban development in the Smart Cities framework.