Calcium phosphate (CaPs)-based nanostructures are mostly known to induce osteogenic differentiation of mesenchymal stem cells (MSCs). However, in the current study, doping of carbon quantum dots into calcium phosphate nanorods (C-CaPs) has been observed to affect the differentiation pathway and enhanced the expression of chondrogenic genes instead of osteogenic ones. Here, we report a microwave-assisted single-step synthesis and doping of carbon dot into calcium phosphate nanorods and their ectopic chondrogenicity in a rodent subcutaneous model. High-resolution transmission electron microscopy, X-ray powder diffraction, and X-ray photoelectron spectroscopy studies show that the doping of carbon dots results in p-type semiconductor-like structure formation at the phosphate site of the bioceramic nanostructure, whereas UV–vis absorption shows a drastic drop in band-gap energy, which enhances the molecular oxygen reduction reaction. The cytocompatibility, free radical scavenging property, and fluorescence microscopy studies proved the applicability of the nanostructure as a cell imaging nanoprobe. Further, fluorescent three-dimensional printed composite scaffolds were prepared and implanted (with MSCs cultured on them) in the rodent model where evidence of ectopic chondrogenesis was observed on the 15th day and 30th day of study via histology and immunohistochemistry. Further, in vitro polymerase chain reaction results and immunohistochemistry results correlated with the physicochemical characterization results. The analysis suggested that doping of carbon quantum dots into CaP nanostructures could activate the HIF-α/SOX-9 pathway for ectopic chondrogenesis.