Organic Cation Transporter 1 (OCT1) mediates the hepatic uptake of a wide range of clinically used compounds. The ability of OCT1 to transport drugs such as the frontline antidiabetic metformin is strongly affected by both genetic polymorphisms as well as drug-drug interactions due to its wide substrate specificity. Despite its importance in drug pharmacokinetics, the substrate selectivity and underlying structural mechanisms of OCT1 function remain poorly understood. Using a combination of structural and functional methods, we provide a comprehensive model to describe both the transport cycle of OCT1 and the mechanism for substrate versus inhibitor specificity to this transporter. Our cryo-EM structures of human OCT1 (61 kDa), resolved to 3.6-2.9 Å resolution, capture both outward- and inward-facing conformations. These structures reveal how conformational changes mediate transport through extracellular and intracellular gates, coupled with charge neutralisation within the binding pocket, that facilitates cationic substrate release (1). Combined with molecular dynamics simulations and functional studies on drug uptake and inhibition, we provide structures of OCT1 complexed with six different compounds that illustrate the chemical basis for transport, affinity and inhibition. Extensive mutagenesis of the binding site of OCT1 reveal how metformin exhibits unique sensitivity to the electronegativity within the pocket, while its hydrophobic analogue phenformin tolerated such substitutions. Our findings lay the foundation for understanding polyspecificity and the mechanism of transport in OCT1, paving the way for better models of drug-drug interactions and the effect of genetic polymorphisms on metformin transport.