Nowadays, legumes are considered as a good source of plant-based proteins to replace animal ones. They are more favorable regarding environmental aspects and health benefits, therefore many people consider moving toward a greener diet. Interestingly, recent consumer trends are promoting pea and faba bean as alternatives to soybean. Both are rich in protein and a good source of essential nutrients and minerals (calcium). However, these advantages can be partially impaired due to their high phytic acid content. This natural polyphosphate is a major antinutrient in plant-based foods, as it can bind minerals (particularly calcium) and proteins, thereby reducing their digestibility and subsequent bioavailability. Indeed, complexes formed are insoluble and limiting the absorption of nutrients, thus lowering the nutritional value of pulses. To understand and overcome these issues, the present review will refine specific mechanisms involved in assemblies between these three essential compounds in legumes as soluble/insoluble binary or ternary complexes. Molecular interactions are influenced by the environmental medium including pH, ionic strength and molar concentrations modulating the stability of these complexes during protein extraction. Protein/phytic acid/calcium complexes stability is of high relevance for food processing affecting not only structure but also functional and nutritional properties of proteins in legume-based foods.