Microglia, the resident macrophages in the central nervous system (CNS), have been intensively studied using rodent genetic models, including the Cre-loxP system. Among them are tamoxifen (TAM)-inducible CX3C chemokine receptor 1 (Cx3cr1)-Cre mouse lines (Cx3cr1^CreERT2), which have enabled in-depth analyses of the biological features and functions of myeloid cells, including microglia. Occasionally, these Cx3cr1^CreERT2 tools have yielded conflicting biological outcomes, the underlying mechanism of which remains unclear. Here, we comparatively characterized the two available Cx3cr1^CreERT2 lines (Cx3cr1^{CreERT2(Litt)} and Cx3cr1^{CreERT2(Jung)}). We find a mouse line-specific and TAM-dependent persistent induction of cyclin-dependent kinase inhibitor 1A (CDKN1A, also known as p21) in microglia of Cx3cr1^{CreERT2(Litt)} mice, but not in those of Cx3cr1^{CreERT2(Jung)} mice, which affects experimental readouts with altered proliferative capacity. Furthermore, aberrant cellular alterations observed in postnatal Cx3cr1^{CreERT2(Litt)} microglia are mitigated by a functional inhibition of CDKN1A. Together, these findings underscore the significance of mouse line-specific phenomena that alter microglial outcomes in a CDKN1A-dependent manner.