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Advancements in single-cell genomics cover a variety of cell types, however the majority happen to be designed for mammalian cells. In this study, a single-cell sequencing pipeline for an intracellular parasite with a small genome of extreme base content was established. This method enables the detection of parasite heterogeneity contributing to malaria parasite adaptation. Early and late-stage parasites from a patient sample were isolated and infected erythrocytes were enriched. To differentiate infected erythrocytes from uninfected, erythrocytes were stained with both SYBR green and MitoTracker Red CMXRos. Cells were seeded onto a CellRaft Array and then single infected erythrocytes were selected and isolated into PCR tubes. By using the CellRaft Array, this study was able to provide a framework for optimizing single-cell amplification and variant analysis in challenging genomes.