Background: In Brazil, 99.7 % of malaria cases occur in the Amazon region. Although the number of cases is decreasing, the country accounted for almost 60 % of cases in the Americas Region, in 2013. Novel approaches for malaria treatment open the possibility of eliminating the disease, but suboptimal dispensing and lack of adherence influence treatment outcomes. The aim of this paper is to show the results on dispensing practices, non-adherence and determinants of non-adherence to treatment of non-complicated malaria. Methods: The study was conducted in six high-risk municipalities with Plasmodium vivax and Plasmodium falciparum transmission in the Brazilian Amazon and based on the theoretical framework of the Mafalda Project, which included investigation of dispensing and adherence. The World Health Organization Rapid Evaluation Method has been used to estimate sample size. Individuals over 15 years of age with malaria were approached at health facilities and invited to participate through informed consent. Data was collected in chart review forms focusing on diagnosis, Plasmodium type, prescribing, and dispensing (kind, quantity, labelling and procedures). Follow-up household interviews complemented data collection at health facility. Non-adherence was measured during the implementation phase, by self-reports and pill-counts. Analysis was descriptive and statistical tests were carried out. Determinants of non-adherence and quality of dispensing were assessed according to the literature. Results: The study involved 165 patients. Dispensing was done according to the national guidelines. Labelling was adequate for P. vivax but inadequate for P. falciparum medicines. Non-adherent patients were 12.1 % according to self-reports and 21.8 % according to pill-counts. Results point to greater non-adherence among all P. falciparum patients and among malaria non-naive patients. More patients informed understanding adverse effects than `how to use' anti-malarials. Conclusions: Non-adherent patients were mostly those with a P. falciparum diagnosis and those in their second or more malaria episode. New taxonomies and concepts on adherence stress the importance of focusing on the individual patient. Interventions targeted to and tailored for malaria patients must be addressed by health policy and implemented by managers and clinicians.