Bifunctional catalysts consisting of metal-containing nanoparticles (NPs) and zeolite supports have received considerable attention due to their excellent catalytic properties in numerous reactions, including direct (biomass is a substrate) and indirect (platform chemical is a substrate) biomass processing. In this short review, we discuss major approaches to the preparation of NPs in zeolites, concentrating on methods that allow for the best interplay (synergy) between metal and acid sites, which is normally achieved for small NPs well-distributed through zeolite. We focus on the modification of zeolites to provide structural integrity and controlled acidity, which can be accomplished by the incorporation of certain metal ions or elements. The other modification avenue is the adjustment of zeolite morphology, including the creation of numerous defects for the NP entrapment and designed hierarchical porosity for improved mass transfer. In this review, we also provide examples of synergy between metal and acid sites and emphasize that without density functional theory calculations, many assumptions about the interactions between active sites remain unvalidated. Finally, we describe the most interesting examples of direct and indirect biomass (waste) processing for the last five years.