Chalcones are organic structures that occur naturally in flavonoids and isoflavonoids from diverse vegetables and fruits. Their properties have promising applications in medicinal chemistry as antiparasitic agents against malaria, leishmaniasis, and Chagas disease. Parasitic diseases, a global health challenge, affect thousands of people around the world. The lack of access to affordable treatments causes many deaths, especially in developing countries. Chagas disease, a neglected infection whose etiological agent is the protozoan Trypanosoma cruzi (T. cruzi), is currently incurable without timely treatment and depends on two primary nitrated chemotherapeutic agents: Nifurtimox (Nfx) and Benznidazole (Bzn). However, these drugs exhibit low selectivity and serious adverse effects, accentuating the critical need to develop new, safer chemotherapeutic options. In this context, herein we report the synthesis of halogen chalcone derivatives by an affordable and sustainable method. In vitro studies against T. cruzi demonstrated that the fluorine-containing structures have the best bioactive profile with inhibitions comparable to Nfx and Bzn. Additionally, ADME analysis was performed to determine the crucial physicochemical and pharmacokinetic descriptors of the series of compounds, which were shown to be suitable for enteral absorption and have a low risk of crossing the blood–brain barrier and damaging brain tissue.