The development of eco-friendly filler materials in membrane-based gas separation technology have become fascinating science that has established a tremendous circular economy. Biogenic silica (BSi) was recovered from rice husks and functionalized using three different molecular structure amine groups in this study. Polyethyleneimine/PEI, N-methylaminopropyl trimethoxysilane/MAPS, and 2-(2-pyridyl) ethyltrimethoxysilane/PETS are used as inorganic fillers for the fabrication of poly (ether-block-amide) (Pebax-1657) mixed matrix membranes (MMMs). The amine functionalized silica and Pebax chains were found to interact through intermolecular hydrogen bonding, tightening the interfacial space and strengthening the thermal stability of the original polymeric membranes. Moreover, the amine groups in each functionalized BSi were sufficient to establish a facilitated transport mechanism for CO2 through the Pebax membranes. Amine functionalized BSi could remarkably upgrade the CO2 permeability (110–120%) and CO2/N2 selectivity (60–70%), surpassing Robeson's upper bound 2008. In addition, Pebax/BSi-MAPS-10 became the most reliable membrane in this study, with CO2 permeability of 90.05 Barrer and CO2/N2 selectivity of 100.41. These findings revealed that amine functionalized BSi was promising for the fabrication of high-quality Pebax MMMs for CO2/N2 separation in industrial applications.