Plastic contamination has become one of the most pressing environmental issues due to rapidly increasing production of disposable plastic products, their fragmentation into smaller pieces, and long persistence in the environment, which affects all living organisms, including plants. In this study, Allium cepa roots were exposed to 0.01, 0.1, and 1 g L−1 of commercial polystyrene (PS-MPs) and polymethyl methacrylate microparticles (PMMA-MPs) for 72 h. Dynamic light scattering (DLS) analyses showed high stability of both types of MPs in ultrapure water used for A. cepa treatment. Morphometric analysis revealed no significant change in root length compared to control. Pyrolysis hyphenated to gas chromatography and mass spectrometry (Py-GC-MS) has proven PS-MPs uptake by onion roots in all treatments, while PMMA-MPs were recorded only upon exposure to the highest concentration. Neither MPs induced any (cyto)toxic effect on root growth and PMMA-MPs even had a stimulating effect on root growth. ROS production as well as lipid and protein oxidation were somewhat higher in PS-MP treatments compared to the corresponding concentrations of PMMA-MP, while neither of the applied MPs induced significant damage to the DNA molecule assayed with a Comet test. Significantly elevated activity of H2O2 scavenging enzymes, catalase, and peroxidases was measured after exposure to both types of MPs. Obtained results suggest that onion roots take up PS-MPs more readily in comparison to PMMA-MPs, while both types of MPs induce a successful activation of antioxidant machinery in root cells that prevented the occurrence of toxic effects.