In this contribution, the synthesis of fluorescent carbon quantum dots (CQDs) by laser fragmentation is reported. To achieve it, an initial suspension of carbon glassy microparticles in polyethylene glycol 200 is irradiated using two different experimental setups, a batch and a flow jet configuration. While the batch configuration is the standard irradiation setup, the flow jet configuration is less extended and it is proposed an implementation with common laboratory material. Besides, this system ensures an improved control over the fluence and the energy delivered to the target, increasing CQDs fabrication rate by 15%. The fluorescence of the generated nanoparticles is measured obtaining an increase of the quantum yield of one order of magnitude. The achieved fluorescence together with their easy cell internalization permits their use as fluorophore. To prove it, the flow jet synthesized CQDs are used for fluorescent imaging of healthy and cancerous human cells. The required incubation time is only 10 minutes and no centrifugation or any other extra processing of the sample is needed. In addition, the fluorescence photostability is measured to be of more than 2 hours in an in vitro application, proving the viability of the generated CQDs even for labeling in applications where long image acquisition times are required.