Fibrillar and spherical aggregates were prepared from whey protein isolate (WPI). These aggregates were thiolated to a substantial degree to observe any impact on functionality. Sulfur-containing groups were introduced on these aggregates which could be converted to thiol groups by deblocking. Changes on a molecular and microstructural level were studied using tryptophan fluorescence, transmission electron microscopy, and particle size analysis. The average size (nm) of spherical aggregates increased from 38 to 68 nm (blocked variant) and 106 nm (deblocked variant) after thiolation, whereas the structure of fibrillar aggregates was not affected. Subsequently, gels containing these different aggregates were prepared. Rheological measurements showed that thiolation decreased the gelation concentration and increased gel strength for both WPI fibrillar and spherical aggregates. This effect was more pronounced upon thiolation of preformed fibrillar aggregates. The findings suggest that thiolation at a protein aggregate level is a promising strategy to increase gelation efficiency.