Over the last few decades, a suite of inorganic proxies based on foraminiferal calcite have been developed, some of which are now widely used for palaeoenvironmental reconstructions. Studies of foraminiferal shell chemistry have largely focused on cations and oxyanions, while much less is known about the incorporation of anions. The halogens fluoride and chloride are conservative in the ocean, which makes them candidates for reconstructing palaeoceanographic parameters. However, their potential as a palaeoproxy has hardly been explored, and fundamental insight into their incorporation is required. Here we used nanoscale secondary ion mass spectrometry (NanoSIMS) to investigate, for the first time, the distribution of Cl and F within shell walls of four benthic species of foraminifera. In the rotaliid species Ammonia tepida and Amphistegina lessonii, Cl and F were distributed highly heterogeneously within the shell walls, forming bands that were co-located with the bands observed in the distribution of phosphorus (significant positive correlation of both Cl and F with P; <). In the miliolid species Sorites marginalis and Archaias angulatus, the distribution of Cl and F was much more homogeneous without discernible bands. In these species, Cl and P were spatially positively correlated (<), whereas no correlation was observed between Cl and F or between F and P. Additionally, their F content was about an order of magnitude higher than in the rotaliid species. The high variance in the Cl and F content in the studied foraminifera specimens could not be attributed to environmental parameters. Based on these findings, we suggest that Cl and F are predominately associated with organic linings in the rotaliid species. We further propose that Cl may be incorporated as a solid solution of chlorapatite or may be associated with organic molecules in the calcite in the miliolid species. The high F content and the lack of a correlation between Cl and F or P in the miliolid foraminifera suggest a fundamentally different incorporation mechanism. Overall, our data clearly show that the calcification pathway employed by the studied foraminifera governs the incorporation and distribution of Cl, F, P, and other elements in their calcite shells.