Currently, plant proteins are fractionated to ingredients with high purities, but an often ignored point is the impact of the extraction and fractionation process on protein functionality. To allow a fair and effective comparison, it is key to understand the changes in protein's aggregated state occurring in the extracted ingredients during processing. We review conventional and upcoming plant protein extraction and fractionation processes (on pulses and oilseeds) and focus on how the processing history influences the macroscopic functional properties of the proteins. To establish this link, we dive into seed morphology and give an overview of the plant seed composition. In addition, we explain the essence of each process step and how it impacts the protein's aggregated state. The latter is linked to the macroscopic functionality (foaming, emulsification, and gelation). We identified three major protein structure-changing steps in the conventional protein extraction process: defatting, alkaline extraction, and isoelectric point precipitation. These steps lead to large, insoluble aggregated structures, which strongly impacts the protein macroscopic functionality. Milder extraction methods reduce these alterations, but a potential consequence is the presence of non-proteinaceous components, which could give challenges in sensory and nutritional aspects and affect the techno-functional properties of the ingredient. The take-home-message is that we need to consider the process-induced change of the protein aggregated structures, which are likely to dominate the functionality over the protein's molecular parameters.