Abstract. Over the last decades a suite of inorganic proxies based on foraminiferal calcite have been developed, of which some are now widely used for paleoenvironmental 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 paleoceanographic parameters. However, their potential as a paleoproxy has hardly been explored, and fundamental insight in their incorporation is required. Here we used nano-scale 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 highly heterogeneous and correlated within the shell walls, forming bands that were co-located with the banded distribution of phosphorus. 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 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 could not be attributed to environmental parameters. Based on these findings we suggest that in the rotaliid species Cl and F are predominately associated with organic linings. We further propose that in the miliolid species Cl may be incorporated as a solid solution of chlorapatite or associated with organic molecules in the calcite. The high F content together with the lack of correlation between Cl and F or P in the miliolid foraminifera suggests 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.