RNA can be chemically modified at a gene-specific level, and this modification has been central to the success of RNA vaccines against COVID-19. Future advances in RNA modifications have substantial promise for RNA vaccines and therapy as well as in optimising recombinant protein expression. However, despite the importance of these modifications in cellular life and their potential biotechnology, the role of the most abundant RNA modifications remains unclear. We have used Nanopore sequencing to interrogate the epitranscriptome in the small unicellular eukaryotic parasite Plasmodium falciparum. This parasite has a small transcriptome with only 3000 genes expressed in any one life stage, making it ideally suited for whole transcriptome analyses. The small genome allows comprehensive transcriptome mapping with individual Nanopore flow cells, and deep sequencing to interrogate the prevalence of RNA modifications, and their correlation with mRNA abundance, mRNA processing, and translational efficiency. Plasmodium transcripts are the most adenosine rich in any known eukaryote, and we find the modification N6-Methyladenosine (m6A) is particularly abundant in Plasmodium mRNA. We have perturbed the writing or reading of this epitranscriptome code by inducibly knocking down the methyltransferase that lays down m6A in mRNA and the reader proteins that detect and decode m6A containing transcripts. These perturbations impact splicing, mRNA abundance, and protein abundance, pointing to nuanced roles for m6A in RNA processing, stability and translational efficiency. The contextual importance of m6A sites remains enigmatic, and we are investigating the impact of methylation position and density within transcripts to better understand how m6A can be effectively exploited as a biotechnology tool.