Current interventions targeting malaria control in sub-Saharan Africa (SSA) are focused on , the most prevalent species infecting humans. Despite renewed efforts for malaria elimination in SSA, little attention has been paid to the neglected parasites and spp. and the impact of interventions like long-lasting insecticidal nets (LLINs), indoor residual spraying (IRS) with non-pyrethroid insecticides, and/or seasonal malaria chemoprevention (SMC) on these minor spp. To address this research gap, this study was undertaken to assess the efficacy of two sequential interventions, IRS and SMC combined with LLINs, on minor- spp. infections in Bongo District, an area characterized by high seasonal transmission in the Northern Sahelian belt of Ghana. Using an interrupted time-series study, five age-stratified surveys, each of ~2,000 participants, were undertaken at the end of the wet seasons between 2012 and 2022. Across this 10-year study period, infections with and spp. were detected using a species-specific PCR targeting the gene. In 2015, following IRS, the prevalence of the minor spp. declined in all ages from baseline in 2012, with participants being significantly less likely to be infected with (13.7% vs 1.4%) and spp. (5.7% vs 0.4%). Despite this decline, in 2017, 32 months after IRS was discontinued and SMC was introduced, the prevalence of (2.9%) and spp. (4.0%) rebounded 2- and 10-fold, respectively. This rebound in the minor species was observed in all age groups, except for the younger children (< 5 years) targeted by SMC. Finally, when we examined this population in 2020 and 2022 after sustained deployment of SMC, the prevalence of continued to increase (7.4% and 5.8%), while the prevalence of spp. declined (2.6% and 1.3%). Results show that both IRS and SMC were effective not only against but also reduced the prevalence of and spp. in Bongo District. Going forward, molecular diagnostics will be critical to identify changes in the submicroscopic reservoir of the minor spp. found in adolescents and adults and to achieve malaria elimination in this region of Ghana.