Nb(0.05 moles%)-zeolites prepared via a post synthesis methodology (BEA, Y, ZSM-5), or a direct sol-gel method (Silicalite-1) were investigated in the hydroxymethylfurfural (HMF) oxidation by both molecular oxygen, in aqueous phase, and organic peroxides, in acetonitrile. The catalysts prepared through the post synthesis methodology (i.e., Nb-Y5, Nb-ZSM25, Nb-Y30, Nb-BEA12, and Nb-BEA18) displayed a mono-modal mesoporosity and contain residual framework Al-acid sites, extra framework isolated Nb(V)O-H and Nb2O5 pore-encapsulated clusters, while Nb-Sil-1, prepared through a direct synthesis procedure, displayed a bimodal micro-mesoporosity and contains only –Nb=O species. These modified zeolites behave as efficient catalysts in both HMF/glucose wet oxidation to succinic acid (SA) and HMF oxidation with organic peroxides to the 2,5-furandicarboxylic acid (FDCA). The catalytic behavior of these catalysts, in terms of conversion and especially the selectivity, mainly depended on the base/acid sites ratio. Thus, the HMF/glucose wet oxidation occurred with a total conversion and a selectivity to SA of 37.7% (from HMF) or 69.1% (from glucose) on the Nb-Y5 catalyst, i.e., the one with the lowest base/acid sites ratio. On the contrary, the catalysts with the highest base/acid sites ratio, i.e., Nb-ZSM25 and Nb-Sil-1, afforded a high catalytic efficiency in HMF oxidation with organic peroxides, in which FDCA was produced with selectivities of 61.3–63.8% for an HMF conversion of 96.7–99.0%.