Nanoplastics (NPs) are prevalent throughout the environment and have raised growing environmental concerns. Although numerous studies have examined the toxicological aspects of NPs, few have investigated their environmental fate and behavior when affected by organisms other than bacteria or fungi. Planktonic ciliates are essential components of aquatic ecosystems and play important roles in decomposing organic matter and transferring energy from the microbial food web to higher trophic levels. To investigate the interplay between NPs and the ciliate Tetrahymena thermophila, we executed a sequence of feeding experiments utilizing 50 nm polystyrene nanoplastics (PS-NPs). In the presence of sufficient nutrition, exposure to PS-NPs (even at concentrations up to 500 mg/L) did not significantly inhibit growth in Tetrahymena thermophila, indicating only a mild toxic effect of PS-NPs. When ingested by T. thermophila, the PS-NPs are repackaged into aggregates with lysosomal components in the food vacuole and finally expelled as compacted "fecal pellets". This process modifies the physical attributes of PS-NPs, including their hydrophilicity, aggregability, and buoyancy, influencing their transportation, retention, deposition dynamics, and ultimately their bioavailability within the environment. A total of 73 proteins were identified from the fecal pellets, containing various hydrolases. Gel permeation chromatography (GPC), Fourier transform infrared (FTIR), and thermogravimetric analysis (TGA) were used to identify changes in molecular weights, functional groups, and thermal stabilities of PS-NP residues in fecal pellets. The results verified the degradation of PS-NPs during the passage through the T. thermophila cell.