Tripartite ATP-independent periplasmic (TRAP) transporters are a major class of secondary transporters found only in bacteria and archaea. Unlike other secondary active transporters, TRAP transporters cannot receive their substrates directly, but do so by using a secreted soluble substrate-binding protein. How a sodium-driven secondary active transporter is strictly coupled to a substrate-binding protein is poorly understood. We report the first high resolution single-particle cryo-EM structures of the sialic acid TRAP transporter SiaQM from both Photobacterium profundum and Haemophilus influenzae at sub-3 Å resolution. These structures reveal the architecture and topology of two structurally distinct forms of TRAP transporter, and further allow us to define “transport” and “scaffold” domains and classify the TRAP as an elevator-type transporter. We find that the SiaQM complex has a unique extended scaffold, allowing TRAP transporters to operate as monomers, rather than oligomers, which are more typical for elevator-type transporters. We define the Na+ and sialic acid binding sites in SiaM, and pinpoint specific lipid binding sites in structures solved in both nanodiscs and amphipol. We confirm a strict dependence on the cognate substrate-binding protein SiaP for uptake, and also report the 1 Å resolution crystal structure of SiaP. Together with co-evolution driven docking studies, transport assays and mutagenesis, these data provide a molecular basis for how sialic acid is delivered to the SiaQM transporter complex. We conclude that TRAP proteins are conceptually a marriage between an ABC importer and a secondary active transporter, which we describe as an ‘elevator-with-an-operator’. These data define TRAP function and informs the design of new antimicrobials against pathogens that use TRAPs during infection.