Despite some previous efforts to study the relationship between urban design and health, the COVID-19 pandemic has attracted more attention on this topic, including all living beings. It has also created awareness of the urgency of reconsidering how cities are designed and lived in. Therefore, the ways of design more resilient cities and rehabilitate them by transforming them into healthier ones and making them become prepared for any possible similar risks in the future are fundamental for post-pandemic cities. This link between cities and health (including mental and physical) might be related to urban morphology, besides environmental and social parameters. This study aims to evaluate the role of the built environment on health and well-being, which affect not only the process of the spread but also the recovering process. In order to achieve this aim, the problem is precisely investigated by focusing the health-related subjects in the context of IMM (Integrated Modification Methodology), which is a holistic, model-based, and objective methodology. In a nutshell, IMM considers the city a complex adaptive system and investigates the integration between its components (i.e., volume, void, links, and types of uses). Key categories represent a functional symbiosis between all the components regarding the functional interdependency between them. Each Key Category is represented by a radar diagram with six quantitative metrics and maps. Performance indicators are the tools that are useful to measure the performance of the existing system. In further steps, Design Order Principles (DOP) is a network of targets aimed to achieve by design. This article will present the metrics (the selected quantitative spatial values that both affect the adaptation and mitigation of the pandemic and contributes to resilient urban design), indicators (e.g., levels of air contaminators, accessibility to open green areas by cycle or foot, features related with biking roads, etc.), to understand the weak parts of the existing structure, and DOPs (e.g., activating an urban metabolism, enhancing biodiversity, promoting walkability and cyclability, etc.) which could be the items in the design process of a more healthy and resilient city for the post-pandemic era. The abandoned railway yard of Farini and surrounding in Milan has been selected as a case study to implement the methodology and eventually make evident how to improve a proposed masterplan