Confiscation of alkaline buffer in a blended cementitious system surges the risk of carbonation. Understanding the carbonation mechanism and kinetics of multi-blended cementitious systems in correspondence to microstructural properties is the need of the hour. In this context, the change in the microstructure of binary, ternary, and quaternary blended cementitious mortar mix comprising of fly ash or/and ultra-fine fly ash or/and nano-silica upon accelerated carbonation (3.5% CO2; 70% RH) was studied. All multi-blended mixes were proportioned using modified Andreasen and Andersen particle packing theory. Permeable porosity and carbonation parameters such as carbonation depth, rate of change in compressive strength, and carbonation shrinkage were measured. Further, qualitative/quantitative estimation of carbonation phases was done using characterization techniques such as TGA and FTIR. In control mix with solely OPC, the reaction of CO2 with calcium-bearing phases showed chemo-mechanical changes leading to 18% improvement in strength at 30 days of exposure. The optimized multi-blended cementitious systems with nano-silica exhibited higher resistance to carbonation kinetics. Phase assemblages quantified through TGA within depth of carbonation imply a negligible concentration of portlandite (CH). However, mixes without nano-silica exhibited a significant reduction in bound water content associated with C–S–H/AFt/AFm phases and intensified the precipitation of calcium carbonate (CaCO3) phase. Asymmetric stretching band of C–O–C at 1424 cm−1 corresponding to calcite phase measured using FTIR validates the outcomes of TGA.