The quaternization of thiophenes through S-alkylation reactions with iodoalkanes in the presence of silver salts opens the door to a new family of room-temperature ionic liquids, yet relatively unexplored in terms of chemical reactivity and applications. This computational study provides a mechanistic rationale that accounts for their formation. The results are consistent with the calculated energy barriers of the corresponding transition structures. Calculations indicate that the geometry at the sulfur atom goes from flat to tetrahedral during salt formation, and the electron delocalization of thiophene is greatly reduced, if not lost, as inferred from aromaticity indexes. Moreover, the rationale explains the influence of polarizable anions on S-alkylation and why alkyl substitution at the α-position of thiophenes gives rise to more stable species than unsubstituted derivatives.