The ‘Malaria Box’ library includes approximately 400 chemically diverse small molecules with well documented potency against malaria parasite growth and replication, however, with the underpinning mechanisms of action remain largely unknown. Using complementary phenotypic screens against Plasmodium falciparum and Toxoplasma gondii, we report phenotype-specific hits based on inhibition of overall parasite growth, apicoplast segregation, and egress or host invasion, providing hitherto unavailable insights into possible mechanisms affected. First, the Malaria Box library was screened against tachyzoite stage of T. gondii and EC50 values for molecules showing ≥80% growth inhibition at 10µM were determined. EC50 comparison between T. gondii and blood stage P. falciparum identified a sub-set of 24 molecules with nanomolar potency against both parasites. Interestingly, 30 molecules that failed to induce acute growth inhibition on T. gondii tachyzoites in a two-day proliferation assay, caused delayed parasitic death upon extended exposure. We demonstrate that at least 3 of these molecules act by interfering with apicoplast segregation during daughter cell formation. Using a complementary approach combining flow cytometry-based analysis and microscopic examinations, we prioritized 26 molecules with inhibitory potential on host cell egress/invasion during asexual developmental stages of P. falciparum. Verification of phenotypes by microscopic examination of Giemsa-stained smears allowed us to further categorize them as specific blockers of egress or invasion. None of the egress/invasion inhibitors affected digestive vacuole integrity, ruling out a mechanism mediated by broadly specific protease inhibitor activity. Intriguingly, 5 of the plasmodial egress inhibitors showed significant inhibition of ionophore induced egress of T. gondii tachyzoites. These findings highlight the advantage of comparative and targeted phenotypic screens in related species, as a means to identify lead molecules with conserved mode of action. Further work on target identification and mechanism will facilitate developing anti-parasitic compounds with cross-species efficacy.