Sugar distribution plays essential roles in plant energy, signaling, and defense mechanisms. Sugar Transport Proteins (STPs) are responsible for proton-driven cellular uptake of glucose, derived from sucrose in the apoplast. Few STPs also facilitate uptake of fructose, the other constituent of sucrose but the molecular features that define differences in specificity are unknown. Here we present a 3.2 Å crystal structure ofArabidopsis thalianaSTP6 in an inward occluded conformational state with glucose bound and show that it is both a glucose and fructose transporter. We perform a comparative analysis with the glucose-selective STP10 usingin-vivoandin-vitrobased systems and disclose how the kinetic transport properties are influenced by different experimental setup. Our work provides detailed insights into the fine-tuned dynamics of affinity-induced specificity for hexose uptake, ultimately showing how the position of a single methyl group in the binding site is sufficient to direct substrate specificity. These findings advance the understanding of hexose trafficking by STPs and extend the framework for engineering STP, and more broadly sugar transport, in the future.