SH‐SY5Y cell line is a model for neural diseases originating from neuroblastoma, a paediatric embryonal malignancy that may differentiate and regress to a benign state. By monitoring the differentiation in single living cells, it could be possible to reach a better understanding of the process and, consequently, to develop new therapeutic approaches. In this work, we investigated the potential of Raman microspectroscopy to monitor biochemical changes in single living SH‐SY5Y cells treated with a combination of retinoic acid (RA) and brain‐derived neurotrophic factor to stimulate the differentiation toward a neuronal phenotype. The results show that the spectroscopic analysis is able to detect biochemical alterations consistent with the differentiation process. Moreover, we investigated also the influence of the cell culture substrate on the treatment outcome. Silicon and aluminium are 2 materials suitable for the spectroscopic analysis and of interest in neuroscience applications. Even though silicon has an ensured biocompatibility, it is subject to alterations after the treatment with RA. Aluminium revealed to be a cost‐effective cell culture substrate for the RA and brain‐derived neurotrophic factor treatment of SH‐SY5Y cells and particularly suitable for Raman microspectroscopy.