Unsaturated porous media, characterized by the combined presence of several immiscible fluid phases in the pore space, are highly relevant systems in nature, because they control the fate of contaminants and the availability of nutrients in the subsoil. However, a full understanding of the mechanisms controlling solute mixing in such systems is still missing. In particular, the role of saturation in the development of chaotic solute mixing has remained unexplored. Using three-dimensional numerical simulations of flow and transport at the pore scale, built upon X-ray tomograms of a porous medium at different degrees of liquid (wetting)-phase saturation, we show the occurrence of chaotic dynamics in both the deformation of the solute plume, as characterized by computed chaos metrics (Lyapunov exponents), and the mixing of the injected solute. Our results show an enhancement of these chaotic dynamics at lower saturation and their occurrence even under diffusion-relevant conditions over the medium’s length, also being strengthened by larger flow velocities. These findings highlight the dominant role of the pore-scale spatial heterogeneity of the system, enhanced by the presence of an immiscible phase (e.g., air), on the mixing efficiency. This represents a stepping stone for the assessment of mixing and reactions in unsaturated porous media.