Quantum dots (QDs) present a special type of nanocrystals (NCs) due to their unique optical and chemical properties. While cadmium-based QDs (Cd-QDs) have the most favorable physicochemical properties, their toxicity, instability in the aqueous phase, and loss of brightness at high temperature are some of the obstacles that prevent the wide use of Cd-QDs. Carbon-based QDs as graphene quantum dots (GQDs) represent a very promising biocompatible replacement. In the present work, we mainly focus on comparing the efficiency and uptake of GQDs and Cd-QDs for fluorescent imaging purposes and studying the effect of growing silica shell on the emission and the uptake of QDs inside living human and bacterial cells. Graphene and CdSe/ZnS QDs were prepared and encapsulated in silica to increase their emission and uptake by living cells. Moreover, we studied their photostability and cytotoxicity. The Prepared G-Si QDs showed good emission inside the cytoplasmic portion of the liver hepatocellular carcinoma cell line (HepG2) and Bacillus subtilis (B. subtilis), but they revealed lower photoluminescence (PL) intensity compared to Si-CdSe/ZnS NCs although G-Si QDs are advantageous in other aspects, i.e. possess lower toxicity and higher stability with temperature variations.