Microplastics (MPs) are ubiquitous and increasing in quantity, causing raising concern. Wastewater treatment plants (WWTPs) are a point source for both aquatic environments and soil, through the use of sludge in agriculture. Understanding the fate of MPs within the wastewater and sludge lines of a treatment plant and, possibly, enhancing their removal will improve the safe reuse of sludge and water effluent and the wastewater biorefinery concept application. This study investigates the effects of alkaline-thermal pretreatment of sludge, followed by anaerobic digestion, on the physical and chemical characteristics of polyethylene terephthalate (PET) and polyamide 66 (PA(66)) contained. Experiments were conducted to evaluate the influence of different NaOH concentrations, temperatures, and reaction times on the degradation of the MPs in anaerobic digestion. PET MPs exhibited relevant mass reduction and structural changes in relation to the NaOH concentration and temperature. PA(66) MPs showed limited chemical alterations, indicating higher resistance to degradation. Batch anaerobic digestion tests of pretreated samples did not modify them further. Chemical characterization of MPs was performed using both Attenuated Total Reflectance-Fourier Transform Infrared spectroscopy (ATR-FTIR) and Focal Plane Array-Fourier Transform-Imaging-Micro-Spectroscopy (FPA-μFTIR-Imaging), revealing distinct trends between surface-level and bulk material changes in the MPs. The results highlighted that ATR-FTIR recorded lower carbonyl index values compared to FPA-μFTIR-Imaging. These findings emphasized the importance of using complementary analytical techniques to thoroughly understand MPs degradation. The outcomes suggest that tailored pretreatment strategies are essential to enhance MPs removal in WWTPs, ensuring safer sludge reuse within a circular economy framework.