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Scanning helium microscopy (SHeM) is an emerging technique that uses a beam of neutral atoms to image and analyse surfaces. The low energies ($\sim$64 meV) and completely non-destructive nature of the probe particles provide exceptional sensitivity for studying delicate samples and thin devices, including 2D materials. To date, around five such instruments have been constructed and are described in the literature. All represent the first attempts at SHeM construction in different laboratories, and use a single detection device. Here, we describe our second generation microscope, which is the first to offer multi-detector capabilities. The new instrument builds on recent research into SHeM optimisation and incorporates many improved design features over our previous instrument. We present measurements that highlight some of the unique capabilities the instrument provides, including 3D surface profiling, alternative imaging modes, and simultaneous acquisition of images from a mixed species beam.