The study of human neural cells, their behaviour and migration are important areas of research in the biomedical field, particularly for potential therapeutic applications. The safety of using neural cells in therapy is still a concern due to a lack of information on long-term changes that may occur. While current methods of cell tracing explore gene manipulations, we elaborate approaches to cell marking with no genetic interference. In this study, we present a novel method for labelling and tracking neural cells using cell-impregnatable photoconvertible polyelectrolyte microcapsules. These capsules demonstrated low cytotoxicity with no effect on the differentiation ability of the neural cells, maintained a high level of fluorescent signal and ability for tracing individual neural cells for over 7 days. The capsules modified with rhodamine- and fluorescein-based dyes were demonstrated to undergo photoconversion by both one- and two-photon lasers while being internalized by neural cells. The finding gives the possibility to select individual capsules inside multicellular structures like spheroids and tissues and alternate their fluorescent appearance. Thus, we can track individual cell paths in complex systems. This new method offers a promising alternative for studying neural cells' long-term behaviour and migration in complex systems such as three-dimensional cellular populations.