Abstract Sustainable construction practices require cementitious materials with high strength that is strongly dependent upon the nature of binding materials and pore structure. The physico-chemical properties of these materials can be tailored suitably by preferential substitution of cement by materials having comparatively small particle size resulting in improved pore structure. This study is aimed to investigate strength and microstructure of the preferentially substituted cement mortars with incorporation of microsilica (MS), nanosilica (NS) and their combined use at 3, 7 and 28 days of curing. The substituent MS (5.0–20%) and NS (0.5–1.25%) have been used at a water binder ratio of 0.5. The specimens were analyzed for the fresh (consistency, setting time, flow) and hardened (compressive and split tensile strength) properties and a correlation between compressive and split tensile strength was obtained. Mortar containing NS was found to develop better strength as compared to the mortar containing MS. The optimum usage of MS with incorporation of NS was further found to increase the strength of mortar significantly. SEM-EDX was used for the analysis of the microstructure of the specimens and the correlation between Ca and Si content was used to analyze the cement matrix. The findings show that the optimized usage of micro and nano silica can give beneficial effects to improve the fresh properties as well as strength with dense microstructure.