The control of multidrug-resistant bacteria (MDRB) is a great challenge in the 21st century. Photodynamic treatment (PDT) is one of the promising approaches to control MDRB. In the process, powerful oxidants such as reactive oxygen species (ROS) are produced, which cause cytotoxic damage and cell death of bacteria. This study examined a new and environment-friendly strategy for the photodynamic inactivation of two MDRB (Escherichia coli and Staphylococcus aureus) and total coliform (TC) in wastewater effluent using two phytochemicals, pyrogallol (PGL) and terpinolene (TPN), along with white and blue light-emitting diode (LED) light. Fourier-transform infrared spectroscopy (FTIR) of the phytochemicals confirmed the presence of different phenolic and aromatic compounds, which can enhance the generation of ROS alongside inactivating the bacterial cells. In the PDT process, white LED light was more active in controlling MDRB than blue LED light. After 80 min irradiation with white LED light (17 mW/cm2), the MDRB bacteria were eradicated completely at a minimum inhibitory concentration (MIC) dose (0.156 mg/mL for E. coli and 0.078 mg/mL for S. aureus) of PGL. In addition, light intensity was an important parameter in photodynamic disinfection. The TC in the secondary effluent was inactivated completely by both phytochemicals after 60 min of exposure to white LED light with an intensity of 80 mW/cm2. The photosensitizing activity of phytochemicals was analyzed by a bactericidal and imidazole-RNO assay. These assays showed that PGL contributed to the generation of •OH radicals, whereas TPN produced 1O2 in the PDT process. Transmission electron microscopy (TEM) confirmed bacterial cell disruption after treatment. Overall, PDT using the phytochemicals as PS is a sustainable approach to control the MDRB and TC in wastewater successfully.