This study explored the influence of high-pressure microfluidization (HPMF) on the structural and functional attributes of apricot kernel protein isolate (AKPI), derived from the deoiled meal of apricot kernels. Single-pass HPMF treatments at 40, 80, 120, and 160 MPa were applied to evaluate pressure-dependent changes in protein morphology, colloidal behavior, molecular structure, and techno-functional properties. HPMF significantly reduced the mean particle size by 78% (from 1362 nm to 259.7 nm) and increased the zeta potential from − 31.2 mV to − 48 mV, enhancing colloidal stability. Scanning electron microscopy (SEM) revealed reduced protein aggregation and a more homogeneous microstructure. Tertiary structural changes assessed via UV–visible and intrinsic fluorescence spectroscopy indicated partial unfolding and exposure of hydrophobic domains up to 80 MPa, with reaggregation observed at higher pressures. At 80 MPa, functional properties were notably enhanced: solubility improved by 26%, emulsifying stability index rose from 67 to 112.5 m²/g, and surface hydrophobicity increased by 30%. Antioxidant potential, measured via DPPH and ABTS assays, increased by 116% and 12%, respectively. In vitro digestibility also improved by 17%, indicating enhanced nutritional bioavailability. Hydrocyanic acid levels in the AKPI were reduced by ~ 88% compared to the meal, suggesting that HPMF can serve as a supportive green detoxification step and can be coupled with the established complementary detoxification treatments. Overall, HPMF particularly at 80 MPa, is a promising non-thermal, biophysical treatment for modulating plant protein structures to improve their functional and nutritional utility in food systems. This work provides mechanistic insights into the structure–function relationship and supports sustainable valorization of plant-based agri-waste.