The rather limited success of translation from basic research to clinical application has been highlighted as a major issue in the nanomedicine field. To identify the factors influencing the applicability of nanosystems as drug carriers and potential nanomedicine, we focused on following their fate through fluorescence-based assays, namely flow cytometry and imaging. These methods are often used to follow the nanocarrier internalization and targeting; however, the validity of the obtained results strictly depends on how much the nanosystem’s fate can be inferred from the fate of fluorescent dyes. To evaluate the parameters that affect the physicochemical and biological stability of the labeled nanosystems, we studied the versatility of two lipid dyes, TopFluor®-PC and Cy5-DSPE, in conventional liposomes utilizing well-defined in vitro assays. Our results suggest that the dye can affect the major characteristics of the system, such as vesicle size and zeta-potential. However, a nanocarrier can also affect the dye properties. Medium, temperature, time, fluorophore localization and its concentration, as well as their interplay, affect the outcome of tracing experiments. Therefore, an in-depth characterization of the labeled nanosystem should be fundamental to understand the conditions that validate the results within the screening process in optimization of nanocarrier.