Multimodal imaging and spectroscopy like concurrent scanning transmission X-ray microscopy (STXM) and X-ray fluorescence (XRF) are highly desirable as they allow retrieving complementary information. This paper reports on the design, development, integration and field testing of a novel in situ atomic force microscopy (AFM) instrument for operation under high vacuum in a synchrotron soft X-ray microscopy STXM–XRF end-station. A combination of μXRF and AFM is demonstrated for the first time in the soft X-ray regime, with an outlook for the full XRF–STXM–AFM combination.