The solid-state fermentation (SSF) of agro-industrial by-products such as okara, pomegranate peel, and cranberry pomace presents a sustainable approach to enhance the release of bioactive compounds. This study investigated the effects of different microbial cultures—Rhizopus oligosporus, Aspergillus oryzae, Streptococcus thermophilus, and a co-culture of R. oligosporus and S. thermophilus—on the bioconversion of bioactive compounds in 100% okara, okara with 2% pomegranate peel, and okara with 1% cranberry pomace. The objective was to assess whether co-culture fermentation with molds and S. thermophilus augments the release of bioactive compounds in okara-based fermentations through synergistic enzymatic activity. Over a period of 72 h, isoflavone transformation (daidzin, daidzein, genistin, and genistein), pH evolution, and water activity were assessed. The co-culture system exhibited improved bioconversion, leading to significant (p < 0.01) increases in daidzein and genistein in pure okara compared to the starting material. The highest polyphenol content (0.908 mg/g) and antioxidant capacity (24.9 mg Trolox eq/g) were recorded in 100% okara. However, pomegranate peel inhibited β-glucosidase activity, delaying the release of isoflavone aglycones. These findings confirm that co-culture fermentation is an effective strategy for enhancing the bioactive properties of okara-based fermentations. This facilitates the release of bioactive aglycones and supports the upcycling of agro-industrial by-products into functional food ingredients. Future research should focus on optimizing fermentation parameters to further enhance the release of bioactive compounds.