Intensive animal production is facing a crisis of legitimacy linked to its contribution to pollution, biohazard risks, and animal suffering. With almost 97% of the production coming from intensive systems, rabbit farming is questioned. Similarly, the plant sector is under scrutiny linked to a high input dependency. Among the alternatives, organic farming and agroforestry systems (associating trees and animals) may contribute to a more sustainable agriculture. However, a number of elements should be evaluated when designing agroforestry systems, especially innovative systems with no previous references. Here, we describe the process of designing an agroforestry system combining rabbits and apple trees. We used an incremental process over three rounds of prototyping (P1, P2 and P3) to develop, refine and adapt a rabbit housing system to an apple orchard. Lessons learned from multiple measurements (thermal comfort, rabbit growth, etc.) and professional feedback (during a workshop) helped to create a functional system. The P1 focused on the design of two outdoor housing systems (mobile-cage vs fixed-pen) inspired by organic rabbit farming practices. Both housing protected the animals from extreme temperatures. However, the main lesson learnt from P1 is the necessity to vaccinate animals to prevent viral diseases. The aim of P2 was to evaluate the feasibility of installing the P1 housing in an apple orchard and to expose it to the observations and comments of professionals during a workshop. On the basis of the experimental observations and the feedback from professionals, the preference was for the fixed-pen over the mobile-cage. The fixed-pen, as opposed to the mobile-cage, allowed the rabbits to graze near the apple tree trunks, where the cleaning services were observed. However, participants questioned the fencing of the fixed-pen. They found it difficult to install and/or dismantle. Based on their comments, the P3 fences were designed to be lightweight and easy to handle. As grazing accounted for about 28% of the rabbits’ activities, and 12 rabbits were able to graze 25.5 m2 of herbage in less than 10 days (P2), the new fencing allowed the fixed-pen to be converted into a mobile-pen. In short, rabbits provide an effective weeding service for the orchard, while benefiting from its microclimate, food resources and living environment, which enhances their well-being. This association was easier to implement in autumn (P2) than in spring (P3), the season of intensive orchard work. In short, this association is feasible and seems to be easily adaptable by farmers.