Autonomous capabilities are required in AmI environments in order to adapt systems to new environmental conditions and situations. However, keeping the human in the loop and in control of such systems is still necessary because of the diversity of systems, domains, environments, context situations, and social and legal constraints, which makes full autonomy a utopia within the short or medium term. Human-system integration introduces an important number of challenges and problems that have to be solved. On the one hand, humans should interact with systems even in those situations where their attentional, cognitive, and physical resources are limited in order to perform the interaction. On the other hand, systems must avoid overwhelming the user with unnecessary actions. Therefore, appropriate user-centered methods for AmI development should be used to help designers analyze and design human-in-the-loop interactions in AmI environments. This paper presents a user-centered design method that defines a process with a set of tools and techniques that supports the process steps in order to systematically design, prototype, and validate human-in-the-loop (HiL) solutions. The process starts with the definition of the HiL design, which defines how the system cooperates with the human. This HiL design is built using a conceptual framework that focuses on achieving human-system interactions that get human attention and avoid obtrusiveness. Then, we provide a software infrastructure to generate a prototype based on the HiL design and validate it by having end-users use a web simulator. The feedback data generated during the prototype user validation is gathered and used by a machine learning tool that infers the user's needs and preferences. Finally, these inferences are used to automatically enhance the human-in-the-loop designs and prototypes. We have validated the proposed method through a twofold perspective: an experiment to analyze the perception of interaction designers regarding their acceptance of the design method and another experiment to evaluate the usefulness of the 'smart' prototyping technique. The results obtained point out the acceptability of the proposed method by designers and the useful adaptations provided by the 'smart' prototyping technique to achieve a HiL design that adapts well to users' preferences and needs.