Microplastic pollution is believed to be one of the most widespread and long-lasting changes on a global scale. Our understanding that microplastics significantly impact terrestrial systems and are a global change stressor continues to grow. In the present study, we investigated the negative effect of long-term (28 days of exposure in food) polystyrene particles of micro (1.0–1.9 µm, 0.4–0.6 µm) and nano (0.04–0.06 µm) scale, in low doses, on the fruit fly – representing a common, globally distributed terrestrial invertebrate, and a model species in many fields. Our observations involved such parameters as ingestion and transfer of particles, survival, reproduction, changes in ultrastructure and tissue and cell responses in midgut epithelium (the place of direct contact with plastic), ovary, and testis in adults, and transgenerational effects in larvae. These observations may indicate possible toxic effects of the tested substances, even in low doses, that can be expected in other taxa, in terrestrial ecosystems. We observed a negative impact of polystyrene particles on the fruit fly survival, midgut, ovary, and testis, involving ultrastructural alterations, such as autophagy and/or ultimately necrosis in the midgut, triggering oxidative stress and activating processes of antioxidative protection. Despite the changes, midgut function and reproduction were not altered – spermatogenesis and oogenesis proceeded normally. The effect was size-dependent – the smaller the polystyrene particles were, the more substantial was the impact they caused. Ultrastructural changes and studied parameters, i.e., generation of ROS (overproduction of which generates oxidative stress), total glutathione concentration (involved in defense against ROS, acting in distinct pathways), and total antioxidant concentration (the oxidative defense system) showed the highest levels after exposure to the smallest nanoparticles, and vice versa. The effect was also sex-dependent, with male flies being more sensitive. Negative effects in males were more substantial and more prominent, even after contact with larger particles, compared to females. The smaller particles (0.4–0.6 µm, 0.04–0.06 µm) were transferred to the ovary and accumulated in the oocytes. In this case, a transgenerational negative effect was detected in larvae. It was characterized by size-dependent alterations, with smaller particles triggering higher levels of ROS and cellular oxidative response. Only the largest particles (1.0–1.9 µm) did not pass into the gonad and did not alter the larvae. These observations together demonstrated that polystyrene particles of micro- and nanoscale, even in a low dose, can induce numerous negative effects on terrestrial invertebrates.