The dimorphic yeast Yarrowia lipolytica has become an emerging cell factory for recombinant proteins production. Expression vectors involving LIP2 promoter (pLIP2) have been developed and used successfully. However, the relationship between dimorphic transition (i.e., cell morphology) and pLIP2 regulation is still unclear and must be assessed to improve process robustness. This requests to discriminate the effect of cell morphology from that of effectors, such as pH, that trigger the dimorphic transition. This was performed using gene reporter system based on β-galactosidase activity and DsRed fluorescence, single-cell analysis by flow cytometry, and quantification of gene expression. Our results clearly pointed out that cell morphology has not effect on the regulation of pLIP2. By contrast, pH modification yielded to phenotypic heterogeneity, potentially leading to a lack of robustness of the cell population. Taken altogether, our results demonstrated that, under appropriate environmental conditions (e.g., pH being an important factor), Y. lipolytica could be considered as a robust and reliable host for recombinant protein production.