The environmental impact is a strong incentive for the development of upcycling processes for textile waste. However, toxic chemicals may occur in both brand-new textiles and post-consumer garments, and the chemical transfer in such routes is important to investigate. The present study applied non-target screening and quantification with liquid chromatography/mass spectrometry to follow the fate of hazardous chemicals from post-consumer polycotton garments to a new material, cellulose nanocrystals, in a chemical upcycling utilizing strongly acidic conditions. The majority of hazardous chemicals detected within the process were found to be transferred to a residual of polyester material and not to the enriched cellulose. However, phthalates were found to be mainly attached to the cellulose nanocrystals. The detected total concentration, in this case, was below 5 μg/g, at least 200 times lower than the limit set by the European Union. This indicates the importance of monitoring and controlling the phthalate content in the starting material of the process, i.e., the post-consumer garments. The chemical release into the process waste effluent could be estimated based on water solubility data for chemicals under the applied conditions. Three compounds, the water-repellent substance perfluorooctanesulfonic acid and the dyes Crystal Violet and Victoria Pure Blue, were almost entirely transferred into the process waste effluent. Although the levels detected were very low in the present pilot process, their presence eventually indicates the need for wastewater purification at further upscaling, depending on the exposure and dose in relation to toxicological relevant thresholds.