Dye pollution is an environmental problem faced by many countries. Dyes such as methylene blue (MB) are harmful and toxic to the environment and human health when they contaminate water. In this study, new composites were fabricated from brown rot fungus (BRF) and MOF UiO-66 immobilized in polyvinyl alcohol and sodium alginate (PVA-SA) matrix to degrade MB dye. BRF species used: Gloeophyllum trabeum (GT) and Daedalea dickinsii (DD), each species mixed with variations of UiO-66 60, 120, and 180 mg. The results showed that the MB decolorization percentages of UiO-66(180)/[email protected] and UiO-66(60)/[email protected] were better than the pure cultures (88.29 ± 0.38% and 72.05 ± 0.57%). While the maximum adsorption capacities (qm) of UiO-66/[email protected] and UiO-66/[email protected] were 0.5510 mg g−1 and 0.3290 mg g−1, respectively, these values were still very low compared to UiO-66. The metabolic products of MB degradation by UiO-66/[email protected] were identified as C16H20N3S (m/z 286), C22H32N3O5S (m/z 450), and C12H13N3O7 (m/z 311). Conversely, the degradation of MB by UiO-66/[email protected] granules produced two metabolites, C16H19N3O2S (m/z 318) and C22H32N3O5S (m/z 450). These results confirm that UiO-66/BRF immobilized on the PVA-SA matrix has the potential to decolorize MB.