While man-made chemicals in the environment are ubiquitous and a potential threat to human health and ecosystem integrity, the environmental fate of chemical contaminants such as pharmaceuticals is often poorly understood. Biodegradation processes driven by microbial communities convert chemicals into transformation products (TPs) that may themselves have adverse ecological effects. The detection of TPs formed during biodegradation has been continuously improved thanks to the development of TP prediction algorithms and analytical workflows. Here, we contribute to this advance by (i) reviewing past applications of TP identification workflows, (ii) applying an updated workflow for TP prediction to 42 pharmaceuticals in biodegradation experiments with activated sludge, and (iii) benchmarking 5 different pathway prediction models, comprising 4 prediction models trained on different datasets provided by enviPath, and the state-of-the-art EAWAG pathway prediction system. Using the updated workflow, we could tentatively identify 79 transformation products for 31 pharmaceutical compounds. Compared to previous works, we have further automatized several steps that were previously performed by hand. By benchmarking the enviPath prediction system on experimental data, we demonstrate the usefulness of the pathway prediction tool to generate suspect lists for screening, and we propose new avenues to improve their accuracy. Moreover, we provide a well-documented workflow that can be (i) readily applied to detect transformation products in activated sludge and (ii) potentially extended to other environmental studies.