The emergence of almond (Prunus amygdalus (L.) Batsch, syn P. dulcis (Mill.)) intensive and semi-intensive cropping systems has created a necessity for new almond cultivars with vigor and shape adapted to these new circumstances. Hence, it is important to unravel which mechanisms are behind the regulation of the tree three-dimensional structure, or tree architecture, and what factors may play a role, like the rootstock choice. In this study, we have analyzed the rootstock influence in the scion transcriptome, regarding the biological processes that control almond tree architecture. 3 commercial almond cultivars were grafted onto 3 hybrid rootstocks, resulting in 9 combinations, whose gene expression in shoot tips were analyzed via RNA-seq. We report that differences in tree architecture phenotype are correlated with differential expression of genes involved in hormonal and molecular responses associated with the regulation of apical dominance, branch formation, plant growth, cell wall formation or nitrogen assimilation. These results highlight the importance of the rootstock choice in the selection of a desirable scion architecture and in the establishment of almond orchards.