Removing aromatic hydrocarbons and heterocyclic compounds from liquid fuels is imperative to comply with increasingly stringent environmental regulations. This study evaluates the efficacy of two betaine-based deep eutectic solvents (DESs) betaine/ethylene glycol (BEG) and betaine/glycerol (BG) for the simultaneous extractive separation of pyridine, thiophene, and toluene from n-heptane. A comprehensive experimental matrix of 65 runs was executed to determine distribution coefficients and selectivity. Statistical analysis demonstrated that the BEG-based system yields a significantly higher extraction capacity than its BG counterpart, a behavior attributed to its lower viscosity and intensified mass transfer kinetics. However, a pronounced capacity-selectivity trade-off was identified in the pyridine–BEG system, where elevated extraction capacities coincided with diminished selectivity due to enhanced n-heptane co-solubility. The separation efficiency followed the decreasing order of pyridine > thiophene > toluene, dictated by specific hydrogen-bonding and acid-base interactions. Ultimately, these insights establish a robust framework for tailoring DES selection relative to the target solute and achieving the optimal balance between solute removal and fuel purity.