Heat-induced protein aggregates act as building blocks for structure formation in pea protein. However, pea protein ingredients are complex mixtures of structurally distinct protein fractions. The interactions among these fractions, before, during, and after heat treatment, remain poorly understood, although they are likely to play an important role in structure formation, including the formation of co-aggregates. Therefore, this study aims to understand the (co-)aggregation behavior of pea protein fractions and the interplay of attractive and repulsive interactions before and after heat treatment at pH 7. First, the pea protein fractions legumin, vicilin, and albumins were isolated, and their thermal properties as well as their individual and co-aggregation behavior were investigated. Zeta potential and surface hydrophobicity measurements provided insights into the balance of attractive and repulsive interactions before and after heat treatment. Furthermore, viscometry allowed the assessment of structural rearrangements and attractive interactions among unheated and heated pea protein fractions. Results indicated that legumin and vicilin aggregate independently, as electrostatic repulsion dominates over hydrophobic attraction upon heat treatment. Albumins, however, exhibited attractive interactions with both legumin and vicilin prior to heat treatment, which promoted the formation of partially insoluble co-aggregates during heating, primarily stabilized via noncovalent bonds. Based on these observations, a mechanism illustrating the (co-)aggregation behavior among pea proteins is proposed. This study provides new insights into the molecular interactions and heat-induced (co-)aggregation behavior among pea protein fractions, thus supporting the targeted application of pea protein ingredients in structure formation.