Rapid emergence of resistance to frontline artemisinin antimalarials underpins the current urgency to discover new antimalarials with novel modes of action. Bis-1,2,4-triazine (bTZ) was discovered as a low-nanomolar hit from a high-throughput screen against blood stage P. falciparum parasites. Compounds from this antimalarial class demonstrate a fast parasite-killing profile and a comparable in vivo infection clearance rate to artemisinin in mice. The mode of action for bTZs remains elusive to date but appears to be novel as no cross-resistance has been observed to a wide range of drug-resistant parasites. Here, we have used a wide range of label-free proteome profiling methods to unravel their mode of action. In order to identify the potential target of bTZs, we used label-free thermal proteome profiling and limited proteolysis-MS on whole parasites. BTZs were found to target specific parasite nuclear proteins, which were then identified to interact with a range of transcription factors and chromatin remodelers using whole-cell crosslinking experiments. We then used phosphoproteomics and methylomics to investigate the function of these proteins perturbed since chromatin remodelling and gene transcription are typically finetuned by post-translational modifications such as phosphorylation, methylation and acetylation. Exposure to bTZs significantly disrupted the phosphorylation and methylation states of several nuclear proteins, subsequently inhibiting their regulatory functions in chromatin remodelling, transcription activation and repression. This was further supported by many nucleic acid binding proteins changing in protein abundance following bTZs treatment. Our work has demonstrated that label-free proteome profiling methods are powerful tools in drug mode of action studies and bTZs are promising novel antimalarial candidates killing P. falciparum parasites via unique mode of action disrupting chromatin remodelling and transcriptional regulation.