This article describes an affordable method for the synthesis of MnMoO₄ nanoflowers through the microwave synthesis approach. By manipulating the reaction parameters like solvent, pH, microwave power, and irradiation duration along this pathway, various nanostructures can be acquired. The synthesized nanoflowers were analyzed by using a powder X-ray diffractometer (XRD), field emission scanning electron microscopy (FE-SEM) with energy dispersive X-ray spectroscopy (EDS), Fourier transform infrared spectroscopy (FT-IR), and UV–vis diffuse reflectance spectroscopy (UV–DRS) to determine their crystalline nature, morphological and functional group, and optical properties, respectively. X-ray photoelectron spectroscopy (XPS) was performed for the examination of elemental composition and chemical states by qualitative and quantitative analysis. The results of the investigations demonstrated that the MnMoO₄ nanostructures with good crystallinity and distinct shape were formed successfully. The synthesized MnMoO₄ nanoflowers were tested for their efficiency as a photocatalyst in the degradation studies of methylene blue (MB) as model organic contaminants in an aqueous medium under visible light, which showed their photocatalytic activity with a degradation of 85%. Through the band position calculations using the electronegative value of MnMoO₄, the photocatalytic mechanism of the nanostructures was proposed. The results indicated that the effective charge separation, and transfer mechanisms, in addition to the flower-like shape, were responsible for the photocatalytic performance. The stability of the recovered photocatalyst was examined through its recyclability in the degradation of MB. Leveraging MnMoO₄’s photocatalytic properties, future studies may focus on scaling up these processes for practical and large-scale environmental remediation.