Malaria is one of the world’s most significant infectious disease. While there have been recent improvements in the number of cases and deaths, in 2016 the World Health Organization reported that >400,000 people died of malaria, mainly children under five. Unfortunately, a widely effective malaria vaccine is not currently available and malaria parasite drug-resistance is a major concern. This means that multi-pronged approaches to malaria prevention and treatment are required if the global goal of malaria eradication is to be achieved. This includes the discovery and development of new drug leads. Histone deacetylases (HDACs), enzymes involved in post-translational modification of eukaryotic proteins, are drug targets for diseases such as cancers, inflammatory diseases and some parasitic diseases like malaria. While a number of potent anti-plasmodial HDAC inhibitors have been identified, the lack of recombinant P. falciparum HDAC enzymes makes target validation and compound prioritization challenging. Assessing effects on histone acetylation by Western blot has been previously used to confirm HDAC inhibitor action in P. falciparum. Here, data are presented on the modification of this approach to a medium-throughput dot-blot format. Instead of carrying out common procedures such as SDS PAGE and western blotting, antigens are placed straight on polyvinylidene difluoride membranes with immunoblotting steps following immediately. This method allows easier comparison of the hyperacetylation effects of anti-plasmodial HDAC inhibitors for compound prioritization and further investigation of promising drug leads.