Increasing population and depletion of resources have paved the way to find sustainable and nutritious alternative protein sources. Pulses have been identified as a nutritious and inexpensive alternative source of protein that can meet this market demand. Pulses can be converted into protein concentrates and isolates through dry and wet separation techniques. Wet extraction results in relatively pure protein isolates but less sustainable due to higher energy requirements and high waste generation. Dry separation focuses on ingredient functionality rather than molecular level purity. These extracted pulse protein ingredients can be incorporated into different food systems to increase the nutritional value and to achieve the desired functionality. But many plant-based alternative proteins including pulses, face several formulation challenges especially in nutritional, sensory, and functional aspects. Native pulse protein ingredients can contain antinutrients, beany flavor, and undesirable functionality. Modification by biological (enzymatic, fermentation), chemical (acylation, deamidation, glycosylation, phosphorylation), and physical (cold plasma, extrusion, heat, high pressure, ultrasound) methods or a combination of these can improve pulse protein ingredients at the macro and micro level for their desired use. These modification processes will thermodynamically change the structural and conformational characteristics of proteins and expect to improve the quality.