With the growing population, access to clean water is one of the 21st-century world’s challenges. For this reason, different strategies to reduce pollutants in water using renewable energy sources should be exploited. Photocatalysts with extended visible light harvesting are an interesting route to degrade harmful molecules utilized in plastics, as is the case of Bisphenol A (BPA). This work uses a microwave-assisted route for the synthesis of two photocatalysts (BiOI and Bi2MoO6). Then, BiOI/Bi2MoO6 heterostructures of varied ratios were produced using the same synthetic routes. The BiOI/Bi2MoO6 with a flower-like shape exhibited high photocatalytic activity for BPA degradation compared to the individual BiOI and Bi2MoO6. The high photocatalytic activity was attributed to the matching electronic band structures and the interfacial contact between BiOI and Bi2MoO6, which could enhance the separation of photo-generated charges. Electrochemical, optical, structural, and chemical characterization demonstrated that it forms a BiOI/Bi2MoO6 p-n heterojunction. The free radical scavenging studies showed that superoxide radicals (O2•−) and holes (h+) were the main reactive species, while hydroxyl radical (•OH) generation was negligible during the photocatalytic degradation of BPA. The results can potentiate the application of the microwave synthesis of photocatalytic materials.