Many molecules exhibit multiple rotational isomers (conformers) that interconvert thermally and are difficult to isolate. Consequently, a precise characterization of their role in chemical reactions has proven challenging. We have probed the reactivity of specific conformers by using an experimental technique based on their spatial separation in a molecular beam by electrostatic deflection. The separated conformers react with a target of Coulomb-crystallized ions in a trap. In the reaction of Ca+ with 3-aminophenol, we find a twofold larger rate constant for the cis compared with the trans conformer (differentiated by the O–H bond orientation). This result is explained by conformer-specific differences in the long-range ion-molecule interaction potentials. Our approach demonstrates the possibility of controlling reactivity through selection of conformational states.