Background <p>More and more forest management focuses on increasing structural complexity to improve environmental conditions for biodiversity and forest functioning. However, it remains uncertain whether animal populations also benefit from increased forest structure. Small mammals are key reservoirs for zoonotic diseases, so understanding how forest structure changes their condition and how this, in turn, affects infection dynamics is critical for animal and human health.</p> Methods <p>This study examined relationships between forest structural complexity, individual body condition (scaled mass index (SMI) and telomere length), pathogen prevalence, and tick load in bank voles and wood mice across 19 forest plots in northern Belgium, representing a gradient of structural complexity.</p> Results <p>Results showed that higher forest complexity, especially with more dead wood and a well-developed herb layer, increased small mammal abundance. Density varied by tree species, with highest abundances in oak and lowest in poplar forests. In addition, body condition improved with structural complexity; SMI increased with woody layer complexity in wood mice and with dead wood availability in bank voles. No clear relationship between telomere length and forest complexity was observed. The relationship between body condition and pathogen prevalence was species- and pathogen-specific. Small mammals in better body condition were more likely to host <i>Borrelia burgdorferi</i> (causing Lyme disease), particularly in complex forests, indicating a higher infection risk with increasing structural complexity.</p> Conclusions <p>Forest management practices that aim to enhance forest structure and biodiversity may thus inadvertently increase zoonotic disease risk and should take these findings in consideration to minimize the risk for human health.</p> Graphical abstract <p></p>