CX3CR1-Cre transgenic mice express Cre recombinase under the direction of the CX3CR1 promoter, and this Cre-lox system is an extensively used tool for genetic manipulations in microglia. Recent studies have highlighted the adverse and off-target effects of inducible CX3CR1-Cre expression on early postnatal microglia like decreased density, increased cell volume and synapse engulfment, with increased anxiety-like behavior in adult mice. However, the possible detrimental effects of constitutive CX3CR1-Cre expression on microglia remain unknown. Here, we thoroughly characterize the effects of constitutive CX3CR1-BAC-Cre expression and find subtle alterations in the morphology of early postnatal and adult microglia, such as decreased cell volume and increased process branching, with no effects on synapse engulfment or anxiety-like behavior in adult mice, unlike inducible CX3CR1-Cre. Our findings have important implications for the use of the CX3CR1-driven Cre-lox system to study microglia, further advocating for the use of controls even when utilizing a well-established genetic tool.