This study investigated the effects of glycine-based (Gly-CNDs) and curcumin-based (Cur-CNDs) carbon nanodots, in combination with mycorrhizal fungi (MF), on the growth and rhizosphere microbiome of tomato plants (Solanum lycopersicum Mill.). The experiment, conducted in 2024 in a controlled greenhouse environment, evaluated root colonization, plant height, stem thickness, chlorophyll content, nitrogen uptake, and microbial abundance in the rhizosphere. Mycorrhizal inoculation significantly enhanced root colonization, particularly when combined with nanodots, improving nutrient uptake and chlorophyll content. The application of Gly-CNDs and Cur-CNDs, both independently and synergistically with MF, positively influenced root biomass, chlorophyll a and b content, and nitrogen accumulation in leaves. Microbial profiling showed that treatments increased bacterial populations (notably Bacillus spp. and Pseudomonas spp.) while suppressing fungal abundance in the rhizosphere, indicating a shift in microbial community structure. Among all treatments, the combination of mycorrhizal fungi with Gly-CNDs (MF+NSG) proved most effective in promoting plant growth and health status. These findings highlight the potential of CNDs as sustainable biostimulants to enhance tomato production, improve soil microbiome dynamics, and reduce reliance on chemical fertilizers.