Despite all efforts, malaria is still highly prevalent in tropical and developing countries. The “test, treat and track” policy of the World Health Organization (WHO) demands the development of affordable and highly sensitive malaria tests that discriminate between the two common malaria parasites, Plasmodium falciparum and Plasmodium vivax, to guide appropriate treatments. In response, we developed a flexible and disposable multielectrode array utilized as electrochemical malaria aptasensor. This multi-target aptasensor was modified by four different aptamer receptors, discriminating between P. falciparum and P. vivax infections via Plasmodium lactate dehydrogenase, expressed by both species, and histidine-rich protein 2, exclusively expressed by P. falciparum. The multi-target aptasensor detection was tested in blood samples spiked with target proteins, whole human blood spiked with P. falciparum, and P. falciparum in vitro cultures. A rigorous analysis revealed sensitivities of >75.0% for 0.001% parasitemia (50 parasites/µL) and a logic gate-based discrimination of Plasmodium infections, overcoming WHO standards. A cost analysis further substantiated the applicability of this multi-target aptasensor as a disposable point-of-care test for remote areas dealing with prevalent malaria parasite infections.