Secondary metabolites obtained from natural sources are medicinally relevant molecules. About one-third of all FDA-approved drugs are derived from or based on natural products, which suggests that molecular optimization is often required for translation from benchtop to clinical practice. Chagas disease, caused by Trypanosoma cruzi, is a neglected tropical disease highly prevalent in Latin America. It has a significant impact on socioeconomic indicators and is not easily cured by the two currently available drugs, benznidazole and nifurtimox. Considering the importance of developing new bioactive molecules based on natural products, this article reviews 21 years of literature reports on the semisynthesis and total synthesis of new compounds targeting T. cruzi. From 1997 to 2018, sixty-six articles reporting five hundred and thirty-seven molecules active against different strains and life stages of the parasite were published. Quinones, alkaloids, terpenes, and lignans were the four largest classes of derivatives, the majority of which had IC50 values low enough to indicate that natural product derivatives can be an important source of potential new drugs to treat Chagas disease. We highlight important molecules in each secondary metabolite class, discussing factors such as selectivity and the basis for their design. An assessment of drug-likeness parameters was performed, which might prove useful for selecting lead compounds for preclinical drug studies.