This study aimed to develop nutritionally enhanced snacks through the synergistic combination of two diverse nutrient sources: milk protein concentrate containing >81% milk protein (MPC81), and a composite source of fiber (>70 wt%) and bioactive compounds (total phenolics, flavonoids, antioxidants, and vitamin C) in the form of agro-industrial byproducts such as apple pomace. Starch and MPC81-based formulations containing 30% (w/w) apple pomace powder were extruded into puffs using supercritical fluid extrusion (SCFX). The effect of SCFX on the retention of bioactive compounds along with the physical, textural, and morphological properties of starch and protein-based extrudates were investigated and compared. Additionally, changes in inter-and intra-molecular interactions among biopolymers during extrusion, and their role in the expansion characteristics of extrudates were also quantified. The resulting MPC81-based extrudates were found to have lighter (0.12 g/cm3 piece density) and softer texture (3.16 kg hardness) compared to starch-based extrudates (0.23 g/cm3 piece density, 12.06 kg hardness), indicating that MPC81-based extrudates containing 30% apple pomace powder offer better functional and sensory-related physical properties. Because of low-temperature (∼25 °C barrel temperature, ∼85 °C product temperature), and low-shear (100 rpm screw speed) along with the use of SC-CO2 as a blowing agent, the resulting extrudates were observed to retain up to 80% total phenolics, 75% antioxidants and 62% vitamin C, which are significantly higher than those reported previously using high-temperature, steam-based cooking extrusion. The FTIR spectra of starch-based formulations indicated a loss of crystallinity and decreased cellulose-lignin interactions, which contributed to the improved extrudate expansion. On the other hand, the expanded protein network was presumably stabilized by an increase in protein aggregation, mainly composed of an elevated β-structure, as confirmed by the FTIR analysis of the protein-based extrudates. The nutritional profile showed that milk protein-based puffs were nutritionally far superior, having significantly higher levels of protein, ash, and fat, as compared to the starch-based puffs. Overall, this study highlights the potential of SCFX to produce milk protein-based extruded products that are nutritionally enriched with agro-industry byproducts such as fruit and vegetable pomace, thereby, adding value to the industrial byproducts streams and lowering the cost of more expensive protein-based products.