The host–guest binding interaction involving two bis-linear tetraamines, namely 1,3-xylenylbis-1,4,8,11-tetraazaundecane (L1) and 2,6-dimethylpyridinylbis-1,4,8,11-tetraazaundecane (L2), with triphosphate and ATP anions is reported. These polyamines, obtained by linking two linear tetraamines with an aromatic spacer, are able to form in aqueous solution and around neutral p[H], very stable complexes with the targeted anionic substrates by means of electrostatic interactions such as hydrogen bonds. This study, investigated by potentiometric and NMR measurements in solution, clearly highlights the different coordination schemes exhibited by these anions according to their inorganic or organic nature; particularly, concerning ATP, the role of the aromatic linker in the complexation, through π-stacking interactions with the adenine part, is evidenced.