The organoleptic fruit quality is crucial to meet consumer requirements. However the market context of these last decades privileged quality criteria having a strong impact on the market value: fruit size, visual aspect and storage potential of fruits. The new challenges to be faced to develop sustainable agriculture encourage to design cropping systems with economic and environmental high-performances, and to produce high quality fruits. Here, we show the interest of integrative approaches to design consistent and relevant cropping systems with regard to multi-criteria objectives. Different case studies are presented using prototyping design, model-based design and multi-criteria evaluation. On peach - nectarine, we show the potential of water management as an important control lever, in connection with tree training and crop load, to design innovative technical scenarios. On apple tree, a cropping system experiment illustrates the multi-criteria evaluation developed to assess orchard systems designed to reduce the use of pesticides. These examples highlight the importance to integrate from orchard conception onwards all the control levers of action to optimize both agronomic and environmental purposes and to perform multi-criteria evaluation of innovative cropping systems to assess their environmental impacts and fruit quality.