Mycelium-based materials are promising environmentally friendly alternatives to synthetic materials. Utilizing industrial fruit and vegetable waste as a low-cost substrate presents a potential pathway for large-scale fungal biomass (FB) production, thereby facilitating the production of mycelium-based materials. In this study, carrot pomace (CP) was used as a substrate for cultivating two filamentous fungi, Rhizopus delemar and Aspergillus oryzae (AO), in bench-scale bioreactors. Harvested solids containing mycelium and CP residues were processed into hybrid paper, mycelium-based paper (MBP), through a wet-laid process. To obtain flexible paper, MBP was then post-treated with glycerol as a plasticizer. Scanning electron microscopy images of the recovered solids showed an interconnected thin microfibrillar structure in AO, whereas Rhizopus delemar demonstrated shorter microfibers with larger diameters. The cross-sectional images of AO-MBP showed a more entangled network structure, with a smaller average pore size (36 μm) compared to RD-MBP (45.7 μm), indicating a more compact microstructure. The tensile strength of AO-MBP was 49 MPa, while RD-MBP displayed a lower tensile strength of 32 MPa. Post-treatment with glycerol reduced average pore size and tensile strength; however, elongation at break was enhanced by 60% for both AO-MBP and RD-MBP compared to untreated samples, resulting in a flexible material suitable for use as wrapping paper. The mechanical properties of MBP were comparable to those of commercial paper products, according to the material property charts. This paves the way for a fungal biorefinery concept for valorizing CP to novel paper-like products with potential applications in packaging.