In this paper, two biosystems based on filamentous fungi and Pd nanoparticles (NPs) were synthesized and structurally characterized. In the first case, results concerning the integration and distribution of Pd-NPs on Phialomyces macrosporus revealed that nanoparticles are accumulated on the cell wall, keeping the cytoplasm isolated from abiotic particles. However, the Penicillium sp. species showed an unexpected internalization of Pd-NPs in the fungal cytosol, becoming a promising biosystem to further studies of in vivo catalytic reactions. Next, we report a new solution-based strategy to prepare palladized biohybrids through sequential reduction of Pd2+ ions over previously harvested fungus/Au-NP composites. The chemical composition and the morphology of the biohybrid surface were characterized using a combination of scanning electron microscopy, transmission electron microscopy, and photoelectron spectroscopy. The deposition of Pd0 over the fungal surface produced biohybrids with a combination of Au and Pd in the NPs. Interestingly, other chemical species such as Au+ and Pd2+ are also observed on the outermost wall of microorganisms. Finally, the application of A. niger/AuPd-NP biohybrids in the 3-methyl-2-buten-1-ol hydrogenation reaction is presented for the first time. Biohybrids with a high fraction of Pd0 are active for this catalytic reaction.