Photo-luminescent carbon dots (CD) have become promising nanomaterials and their synthesis from natural products has attracted attention by the possibility of making the most of affordable, sustainable and, readily-available carbon sources. Here, we report on the synthesis, characterization and bioimaging potential of CDs produced from diverse extensively produced fruits: kiwi, avocado and pear. The in vitro cytotoxicity and anticancer potential of those CDs were assessed by comparing human epithelial cells from normal adult kidney and colorectal adenocarcinoma cells. In vivo toxicity was evaluated using zebrafish embryos given their peculiar embryogenesis, with transparent embryos developing ex-utero, allowing a real-time analysis. In vitro and in vivo experiments revealed that the synthesized CD presented toxicity only at concentrations of ≥1.5 mg mL−1. Kiwi CD exhibited the highest toxicity to both cells lines and zebrafish embryos, presenting lower LD50 values. Interestingly, despite inducing lower cytotoxicity in normal cells than the other CDs, black pepper CDs resulted in higher toxicity in vivo. The bio-distribution of CD in zebrafish embryos upon uptake was investigated using fluorescence microscopy. We observed a higher accumulation of CD in the eye and yolk sac, avocado CD being the ones more retained, indicating their potential usefulness in bio-imaging applications. This study shows the action of fruit-based CDs from kiwi, avocado and pear. However the compounds present in these fruit-based CDs and their mechanism of action as a bioimaging agent need to be further explored.