Tree crops are explored for food sources and raw materials for industrial sectors. However, breeding tree species to meet current economic demands amid forecasts of agricultural resource scarcity and climate instability is a challenging task. This is especially true due to their long juvenile phase, often difficulties related to reproductive biology, and scarcity of genetic resources, which largely delays phenotyping and selection of segregating populations. On the other hand, genome sequence and transcriptomic data are becoming increasingly available for perennial crops, along with optimized protocols for genetic transformation and in vitro regeneration. Due to the development of these fields altogether and the advances in gene editing technologies, it is now possible to glimpse the design of tree crops with optimized traits for cultivation. We review the status of genome projects and the application of CRISPR-Cas-based systems in tree crops, alongside an exploration of gene editing technologies to develop perennial crop ideotypes. Herein, we seek to raise attention to the capabilities and potential of crop designing applied to tree species and to the opportunity that we have, as a society, to create stepwise strategies to tailor the breeding of perennial crops in the context of the current environmental challenges and increasing population demands.