Reconstructing the evolutionary dynamics of natural populations requires an understanding of the geographical distribution of nuclear and mitochondrial genetic diversity. The analysis of these two genetic markers frequently discloses discordant patterns (mito-nuclear discordance) that can arise simply as a consequence of their different effective population sizes (Ne). Species-specific sex-biased dispersal may contribute to the mito-nuclear discordance observed in natural populations. However, the relative contribution of genetic drift versus sex-biased dispersal in driving mito-nuclear discordance remains insufficiently evaluated. Here, we use forward genetic simulations to address this knowledge gap. Our findings support the baseline level of mito-nuclear discordance arising from distinct genomic Ne, but show that this inherent discordance is magnified by sex-biased dispersal patterns. We demonstrate that female-biased dispersal leads to a marked spatial mismatch between mitochondrial and nuclear diversity across the simulated populations, thereby reducing the spatial concordance between mitochondrial and nuclear markers. Conversely, male dispersal patterns appear to increase, although to a reduced degree, the intrinsic level of discordance between nuclear and mitochondrial geographical marker distribution. Our results highlight the importance of integrating the intrinsic characteristics of nuclear and mitochondrial genomes and the impact of sex-biased dispersal for accurately interpreting patterns of genetic diversity and reconstructing evolutionary histories.