Protein stability in ionic solutions depends on the delicate balance between protein–ion and ion–ion interactions. For molecular ions containing multiple charged groups, the role of ion–ion interactions is particularly important. In this study, we show how the interplay between homo- and heteroion pairing influences protein stability using polyarginine salts as a model system. For the chloride salts, protein thermostability decreases as the size of the peptide increases, indicating enhanced binding to the protein. Moreover, it indicates reduced homoion pairing between Gdm+ and carboxylate groups that is largely responsible for aggregation suppression, rather than denaturation, in monomeric arginine solutions. However, for the sulfate salts, strong heteroion pairing between the Gdm+ groups and the sulfate counterions compensates for the loss of homoion pairing and, in return, leads to enhanced thermostability and a dramatically reduced (up to 10–30 times) rate of protein aggregation. Molecular dynamics simulations reveal how this ion pairing enhances conformational stability and, at the same time, reduces protein association. This study provides insight into complex ion effects on protein stability and serves as an example of how these intrasolvent interactions can be leveraged to enhance protein stability.