Cyanobacteria possess highly efficient CO2-concentrating mechanisms (CCMs) that improve photosynthetic performance under low or fluctuating CO2 conditions. While the individual components of cyanobacterial CCMs are well characterised, the mechanisms by which the CCM is regulated in response to changing environmental CO2 concentrations remain poorly understood. In previous work we have shown that a PII-like protein, SbtB, regulates the activity of the cyanobacterial sodium-dependent bicarbonate transporter, SbtA. Here, we present isothermal titration calorimetry and SDS-PAGE analysis data to show that SbtB from Cyanobium sp. PCC 7001 (SbtB7001) binds cAMP, AMP, ADP and ATP with low micromolar affinities, and that these effector molecules control the association and dissociation of the SbtA-SbtB complex in vitro. High resolution X-ray crystal structures of SbtB7001 in the apo- and ligand-bound states reveal that binding of ATP stabilises an otherwise flexible and disordered ‘T-loop’ region that is important for protein-protein interactions in related PII-like regulatory proteins. We present a new model for the regulation of SbtA-mediated bicarbonate transport by SbtB, which we hope will aid efforts to incorporate components of cyanobacterial CCMs into the chloroplasts of C3 plants to improve photosynthetic performance and crop yields.