Commercial pea protein isolates tend to form weak, heat-induced gels, limiting their application in solid plant-based dairy alternatives. Enzymatic cross-linking with microbial transglutaminase (mTGase) is a promising approach to improve gelation. However, its efficiency depends on the balance between protein unfolding and aggregation. Partial denaturation exposes reactive sites, while excessive aggregation reduces solubility and enzyme accessibility. This study investigated how the interplay between protein solubility, aggregation state and particle size governs mTGase-induced cross-linking and gel properties of high-protein pea emulsions. Two commercial protein isolates, B9 and HV, were separated into water soluble (supernatant) and insoluble (sediment) fractions, freeze-dried, and characterized. Emulsion gels containing 15% (w/w) protein powder and 10% (w/w) oil were prepared with (10 U/g) or without mTGase. Gelation behavior and cross-linking at the molecular scale were assessed using oscillatory rheology and SDS-PAGE. Highly soluble proteins with small particle sizes and a higher abundance of low-molecular-weight fractions (B9 supernatant) showed the highest gelation rate and formed stiff, elastic, and strong gels with a tough texture. In contrast, poorly soluble, aggregated proteins (isolates and sediment fractions) showed little rheological improvement after mTGase treatment. Using the difference in complex modulus between mTGase-treated and reference samples (ΔG∗) enabled separation of enzymatic from non-enzymatic stiffening and provided a kinetic measure of cross-linking efficiency. SDS-PAGE revealed that all samples contained suitable mTGase substrates (globulins ≥35 kDa), which disappeared after mTGase treatment, confirming that cross-linking occurred at the molecular scale. In conclusion, solubility and particle size should be considered or tailored when developing plant-based foods using mTGase.