Background Innate immune cells including γδ T-cells and NK cells are directly activated by Plasmodium falciparum parasites and contribute to the control of parasitaemia. The aim of this study was to determine whether a history of parasite exposure and/or carriage affect innate immune cell responses in vitro to P. falciparum infected red blood cells (PfRBC). Methods Peripheral blood mononuclear cells were collected from 61 Malian children aged 5 to 15 years at the start of the transmission season, and 10 malaria-naïve Dutch adults. Parasite carriage at the start of the transmission season was assessed by PCR and microscopy for Malian children. Peripheral blood mononuclear cells were stimulated with PfRBC to assess cytokine production and degranulation of innate lymphocytes (γδ T-cells, CD3+CD56+ cells and NK cells) by flow cytometry. Results Granzyme B production in response to PfRBC was observed by all three innate cell subsets in Malian children, as were IFNγ production by γδ T-cells and NK cells and γδ T-cell degranulation. However, both IFNγ production and degranulation by γδ T-cells, CD3+CD56+ cells and NK cells were significantly lower compared to malaria-naïve Dutch adults. Moreover, children with ongoing P. falciparuminfection showed significantly reduced PfRBC-specific IFNγ production and degranulation by γδ T-cells and NK cells as compared with those with undetectable parasitaemia by PCR and microscopy. Reduced degranulation responses by γδ T-cells and NK cells were already observed for children with submicroscopic parasitaemia as compared to those with negative PCR. Conclusions Malian children show reduced P. falciparum-specific innate IFNγ production and cytotoxic degranulation, which were further negatively impacted by ongoing infections of microscopic but also submicroscopic parasitaemia.