This study explores the effects of different types of nanoparticles, namely nano-SiO₂ (NS), nano-TiO₂ (NT), and nano-Fe₂O₃ (NF) on the fresh properties, mechanical properties, and microstructure of cement mortar containing fly ash as a supplementary cementitious material. These nanoparticles existed in powder form and were incorporated into the mortar at the dosages of 1%, 3%, and 5% wt.% of cement. Also, fly ash has been added into in mortars with a constant dosage of 30% wt.% of cement. Compressive and flexural strength tests were performed to evaluate the mechanical properties of the mortar specimens with different nanoparticles at three curing ages, 7, 14, and 28 days. Scanning Electron Microscopy (SEM) and Energy Dispersive X-ray (EDX) tests were conducted to study the microstructure and the hydration products of the mortars. To elucidate the effects of nanoparticles on the binder phase, additional experiments were performed on accompanying cement pastes: nanoindentation and open porosity measurements. The study shows that, if added in appropriate amounts, all nanoparticles investigated can result in significantly improved mechanical properties compared to the reference materials. However, exceeding of the optimal concentration results in clustering of the nanoparticles and reduces the mechanical properties of the composites, which is accompanied with increasing the porosity. This study provides guidelines for further improvement of concretes with blended cements through use of nanoparticles.