Introduction Seasonal malaria chemoprevention (SMC) is a highly effective intervention for malaria prevention in high burden areas with seasonal transmission, historically implemented in the Sahel. Mozambique contributes to 4% of global malaria cases, malaria being one of four major causes of mortality nationally. The mid-term review of the Malaria Strategic Plan 2017–2022 recommended SMC in Mozambique. Malaria Consortium, in partnership with the National Malaria Control Program, conducted a two-year phased SMC study in Nampula province using sulfadoxine-pyrimethamine (SP) plus amodiaquine (AQ), or SPAQ, in children under five. Phase one investigated acceptability, feasibility, and protective effect of SMC; while phase two, researched the effectiveness of SMC, chemoprevention efficacy and changes in resistance markers prevalence. The following references phase one results.Methods A pragmatic type II hybrid effectiveness-implementation study design was adopted, using mixed methods. The study was conducted in three districts, utilising: (1) non-randomised controlled trial; (2) drug resistance molecular marker study; (3) coverage and quality assessment; and (4) acceptability and feasibility assessment with stakeholders.Results Children who received SMC had 86% (hazard ratio 0.14, 95% CI: 0.09–0.24) lower hazards of developing clinical malaria during the peak transmission season compared with children in the comparison district. Prevalence of SP molecular markers associated with resistance was high at baseline (K540E 66.1%). However, a non-statistically significant trend of increasing prevalence was observed. SMC achieved high coverage of eligible children over four cycles (87.7%, 95% CI: 83.9%-90.8%). Qualitative results indicate SMC was positively accepted by the targeted community, with few negative opinions reported.Conclusions Results suggest that SMC was effective at preventing clinical malaria, did not significantly impact resistance profile, and was feasible and acceptable in the context. Phase two will assess SMC impact in reducing malaria incidence and if chemoprevention efficacy of SPAQ is impacted by drug resistance and drug concentrations.