A majority of works developed in apple tree architecture and physiology in past decades are based on trees grown in monocultivar high density orchards. Here we propose to connect knowledge on the tree itself with knowledge on the system in which it is grown. In the two cases, scientific advances are intrinsically connected with practical aspects. It is first shown that although whole-tree shape variability presents a descriptive interest it is not strictly related to the fruiting pattern which is a major issue for apple cultivation. Architectural analyses have been developed not only to gain knowledge on the dynamics of tree growth and branching but also to analyze thoroughly the physiological conditions for an optimized fruit-set, fruit quality and return-bloom. Shoot length and the physiological abortion of young shoots on the same branch (extinction) have been shown as two main components for regular yield and high quality fruiting. These architectural analyses have also been at the origin of an innovative pruning procedure, artificial spur extinction, developed under the paradigm of precision horticulture. It is implemented in various training systems. The sustainability of intensive apple growing systems is now questioned, especially because of their high dependency on external inputs whether phytosanitary products or fertilizers. Agroforestry, i.e., growing woody perennials and annuals in spatial mixtures or temporal sequences, is proposed as a means to reduce such dependencies. It uses plant biodiversity to enhance ecological services including multiple cropping. For apple, the social-economic acceptability and performance of such systems have certainly to be investigated. From the horticulture point of view, this new context challenges the choice of plant material and also of training and pruning concepts developed in intensive orchards. From the scientific point of view apple tree based agroforestry systems address architectural and physiological issues on how the apple tree can develop and fruit satisfactorily in such biotic and abiotic contexts.