The transition from animal-based proteins to plant-based alternatives is essential to address environmental concerns and promote sustainable food systems. Plant-proteins are mainly available as either concentrates (~50-80% protein) or isolates (>80% protein), which vary not only in purity and composition but also in their protein structural organization and functionality, concurrently associated with their extraction method and source. To unravel these effects, the heat-processing behavior of two protein sources were studied: sunflower, a by-product of oilseed extraction, and lupin, a protein-rich legume with high fiber content. These proteins were evaluated as concentrates (50–53% protein), along with their corresponding laboratory-prepared isolates, obtained by alkaline extraction-isoelectric precipitation (80–85% protein), which were systematically compared to commercially available lupin and sunflower protein isolates (90–92%). The proteins were characterized for their nativity, molecular weight, globulin/albumin fractions, surface hydrophobicity, solubility, and gelation to establish structure–function relationships. To evaluate their gelation behavior, the 6 proteins were subjected to hydrothermal processing under high-moisture (20% solids), low-shear conditions at either 95 °C or 140 °C, representing moderate and severe heat-treatments. The processed samples were analyzed for microstructure and protein solubility. The studied proteins differed in subunit composition: sunflower proteins and the commercial lupin isolate were mainly composed of 11S legumine-like globulins, whereas lupin concentrate and its laboratory isolate contained both 7S and 11S globulins, with a 7S predominance. Notably, only the commercial sunflower isolate was pre-denatured, while the others were native, enabling assessment of the effect of protein nativity on functional behavior. Regarding surface hydrophobicity, the extraction method had a clear impact, with both commercial isolates being the most hydrophobic, especially the pre-denatured sunflower isolate. Sunflower and lupin concentrates exhibited intermediate levels, while the laboratory isolates showed the lowest hydrophobicity due to their carefully controlled isolation conditions. After hydrothermal processing at 95 °C, sunflower concentrate showed the highest gel viscosity, followed by its laboratory isolate, while the commercial isolate exhibited an almost flat profile near zero throughout the measurement. Meanwhile, lupin concentrate and its laboratory isolate exhibited similar heat-viscosity profiles with much lower gel viscosity than sunflower proteins. Conversely, the commercial lupin isolate showed only a brief initial increase due to cold-water absorption, followed by very low viscosity. During hydrothermal processing at 140 °C, sunflower concentrate displayed higher viscosity but also greater breakdown and lower final viscosity than at 95 °C. Both sunflower isolates, particularly the commercial one, exhibited a spiky viscosity profile during cooling, indicating protein aggregation. In contrast, lupin concentrate displayed a second peak not observed at 95 °C or in its laboratory isolate at 140 °C, suggesting contributions from non-protein components or dissembling and solubilization of larger protein aggregates. The commercial lupin isolate showed higher final viscosity compared to its near-zero viscosity at 95 °C, although it did not reach gel formation (below least gelation concentration). Microscopy revealed larger aggregates in sunflower samples with increasing heat-treatment, likely due to the predominance of 11S globulins, whose hydrophobic nature and disulfide bonds could promote further re-aggregation. Meanwhile, lupin samples remained more homogeneous across treatments, with only slightly coarser particles at 140 °C, mainly in the isolates. Protein solubility (indicative of the protein fraction not contributing to the network) generally decreased under severe heat conditions, except for the sunflower laboratory isolate, which remained stable, and both commercial isolates, which increased at 140 °C, suggesting a higher protein de-aggregation during high temperature conditions. Overall, these findings demonstrate how protein origin, purity, and structure influence structural changes and gelation during heat processing, underscoring the importance of thorough ingredients characterization, and providing a deeper understanding for the design of plant-based food systems with enhanced functionality.