A recognized problem in profilometry applied to artworks is the spatial referencing of the surface topography at micrometer scale due to the lack of references in the height data with respect to the “visually readable” surface. We demonstrate a novel workflow for spatially referenced microprofilometry based on conoscopic holography sensors for scanning in situ heterogeneous artworks. The method combines the raw intensity signal collected by the single-point sensor and the (interferometric) height dataset, which are mutually registered. This dual dataset provides a surface topography registered to the artwork features up to the precision that is given by the acquisition scanning system (mainly, scan step and laser spot). The advantages are: (1) the raw signal map provides additional information about materials texture, e.g., color changes or artist marks, for spatial registration and data fusion tasks; (2) and microtexture information can be reliably processed for precision diagnostic tasks, e.g., surface metrology in specific sub-domains and multi-temporal monitoring. Proof of concept is given with exemplary applications: book heritage, 3D artifacts, surface treatments. The potential of the method is clear for both quantitative surface metrology and qualitative inspection of the morphology, and it is expected to open future applications for microprofilometry in heritage science.