Multispecies horticultural systems were traditional in both tropical and temperate regions for millennia, mixing for example fruit trees and vegetables. They have been progressively replaced, especially after World War II, by monocropping horticulture. These specialized systems are highly productive but also need high nutrient and phytosanitary inputs. There is now an increasing interest for biodiversity-based agrosystems with the assumption that increasing plant functional diversity in and around the plot is an efficient lever to reduce these inputs. Indeed, biodiversity is put forward as a way to promote various ecosystem services, including pest regulation and nutrient recycling, and is at the core of agroecology concepts developed a century ago. However, combining agricultural plants grown for production and “companion” plants grown for other services in the same plot needs more study on how the agricultural plant is affected by a generally more competitive context. The focus of our study was the effects of shade, known as a main factor characterizing multispecies systems, especially agroforestry systems, on tree architecture and flowering of a temperate and a tropical species, apple and mango. Overall, our results showed that the effects of the light environment, possibly modified by a diversified agrosystem, has a key role on the architecture and functioning of the agricultural plant, affecting both vegetative and reproductive compartments, and their relationships. This is especially true for fruit trees for which there are carry-over effects across years related to the perennial structural framework. Our study therefore strongly suggests that to strengthen the potential agronomic interest in diversified agrosystems, the holistic view at the core of the system approach needs to be complemented by more knowledge on how the agricultural plant interacts with its biotic environment.