Understanding complex biological systems requires functional characterization of specialized tissue domains. However, existing strategies for generating and analyzing high-throughput spatial expression profiles were developed for a limited range of organisms - primarily mammals. We present the first available approach to generate and study high-resolution, spatially-resolved functional profiles in a broad range of model plant systems. Our process includes high-throughput spatial transcriptome profiling followed by spatial gene and pathway analyses. Here we first demonstrate feasibility by generating spatial transcriptome profiles from model angiosperms and gymnosperms microsections. In Arabidopsis thaliana we use the spatial data to show differences in expression levels of 141 genes and 189 pathways among eight inflorescence tissue domains. Our combined approach of spatial transcriptomics and functional profiling represents a powerful new strategy that can be applied to a broad range of plant species, providing an approach that will be pivotal to answering fundamental questions in developmental and evolutionary biology.