Abstract This study investigates the valorization of Capparis ovata seeds as a sustainable source of high-quality plant protein. Protein powders were produced via four extraction methods: standard alkaline (CAE), enzyme-assisted (EAE), ohmic heating-assisted (ODE), and a combined ohmic heating-enzyme-assisted process (CODE-EE). Structural characterization using FTIR and SEM revealed preserved protein conformations and distinct morphological features across methods. SDS-PAGE analysis indicated molecular weights of 19–47 kDa. Amino acid profiling demonstrated high levels of essential amino acids, including isoleucine, leucine, lysine, tryptophan, glutamic acid, and arginine, with ohmic heating and enzyme treatments enhancing their abundance. The extraction method significantly influenced techno-functional properties: CODE exhibited the highest water-holding and oil-holding capacities (WHC: 3.18 g/g; OBC: 3.64 g/g), CODE and CODE-EE achieved maximal foaming capacity (110.0% ± 2.0 and 109.0% ± 1.0), and CODE-EE showed superior emulsifying activity and stability, whereas CAE displayed the lowest performance. The exciting potential of caper seeds as a valuable plant-based protein source is demonstrated by this study, which also reveals how the CODE-EE process efficiently yields protein powder with a high protein content and superior functional qualities.