Presently, there is a need for development of cleaner and sustainable tanning system by introducing biocompatibility and degradability to the leather without affecting its physical properties. Particularly, tanners seek chrome-free tanning systems due to their cleaner image, market demand, and good physical properties. Amongst tanning agents, silica and its combination have been identified as a greener tanning system. In the present study, a combination tanning system based on surface modified silica and aldehyde has been developed. The main invention lies in identifying a new tanning system based on silica with an amine terminal followed by dialdehyde post treatment with an appropriate post-tanning process. Initially, the silica will stabilize the collagen fibres through multiple hydrogen bonding and electrostatic interactions. Later, adding aldehyde enhances the bonding between silica and collagen through multiple intermolecular crosslinking. This was further validated by the molecular interaction studies of collagen with a silica-glutaraldehyde combination system. This developed chrome-free tanning process produces leathers exhibiting reasonable thermal stability of around 90 °C with reduced chemical oxygen demand (COD) load and no chromium in the wastewater. Due to the synergistic effect of silica and aldehyde, even the tanned leather exhibited improved antimicrobial activity against gram-positive Bacillus subtilis and gram-negative Escherichia coli. One of the main benefits of this new tanning system is the lower environmental impact with an E-factor of 0.23. Sustainability indicators suggest that the tanning by silica combination found to be environmentally friendly and cost effective method as compared to conventional chrome tanning process.