Mesoporous silica nanoparticles (MSNs) have attracted great interest for last two decades due to their unique and advantageous structural properties, such as high surface area, pore volume, stable mesostructure, tunable pore size and controllable particle morphology. The robust silica framework provides sites for organic modifications, making MSNs ideal platforms for adsorbents and supported organocatalysts. In addition, the pores of MSNs provide cavities/ channels for incorporation of metal and metal oxide nanoparticle catalysts. These supported metal nanoparticle catalysts benefit from confined local environments to enhance their activity and selectivity for various reactions. Biomass is considered as a sustainable feedstock with potential to replace diminishing fossil fuels for the production of biofuels. Among several strategies, one of the promising methods of biofuel production from biomass is to reduce the oxygen content of the feedstock in order to improve the energy density. This can be achieved by creating C-C bonds between biomass derived intermediates to increase the molecular weight of the final hydrocarbon molecules. In this context, pore size and organic functionality of MSNs are varied to obtain the ideal catalyst for a C-C bond forming reaction: the aldol condensation. The mechanistic aspects of this reaction in supported heterogeneous catalysts are explored. The modification of supported organocatalyst and the effect of solvent on the reaction are rationalized. The significance of two functional surfaces of MSNs is exploited by enzyme immobilization on the external surface and organo catalyst functionalization on the internal surface. Using this bifunctional catalyst, the tandem conversion of small chain alcohols into longer chain hydrocarbon molecules is demonstrated. The ability to incorporate metal and metal oxide nanoparticles in the pores and subsequent functionalization led to develop organic modified magnetic MSNs (OM-MSNs) for applications in microalgae biorefinery. Two different integrated biorefinery systems are highlighted. (i) OM-MSNs are used to harvest microalgae and selectively sequester free fatty acids (FFAs). (ii) OM-MSNs are shown to selectively sequester FFAs and convert them into diesel-range liquid hydrocarbon fuels. A similar MSN supported metal nanoparticle catalyst is demonstrated to transform FFAs into green diesel with even greater activity and selectivity. The incorporation of a different organic functional group into MSN provides a selective adsorbent for separation and purification of ?-tocopherol from microalgae oil. The functional group with electron deficient aromatic rings demonstrated high sequestration capacity and selectivity of {alpha}-tocopherol.