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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 in high vacuum in a synchrotron soft X-ray microscopy STXM-XRF end-station. A combination of XRF-AFM is demonstrated for the first time in the soft X-ray regime, with an outlook for the full XRF-STXM-AFM combination.