How molecular patterning scales to organ size is highly debated in developmental biology. We explore this question for the characteristic gene expression domains of the plant stem cell niche residing in the shoot apical meristem. We show that a combination of signals originating from the epidermal cell layer can correctly pattern the key gene expression domains and notably leads to adaptive scaling of these domains to the size of the tissue. Using live imaging, we experimentally confirm this prediction. The identified mechanism is also sufficient to explain de novo stem cell niches in emerging flowers. Our findings suggest that the deformation of the tissue transposes meristem geometry into an instructive scaling and positional input for the apical plant stem cell niche.This work was funded by grants from the Gatsby Charitable Foundation (GAT3395/PR4) and the Swedish Research Council (VR2013-4632) to HJ; and by Gatsby Charitable Foundation grants GAT3272/C and GAT3273-PR1, the US National Institutes of Health (R01 GM104244), the Howard Hughes Medical Institute, and the Gordon and Betty Moore Foundation (GBMF3406) to EMM).This is the final version of the article. It first appeared from the American Association for the Advancement of Science via http://dx.doi.org/10.1126/sciadv.150098