Mass spectrometry imaging (MSI) has shown to bring invaluable information for biological and clinical applications. However, conventional MSI is generally performed ex vivo from tissue sections. Here, we developed a novel MS-based method for in vivo mass spectrometry imaging. By coupling the SpiderMass technology, that provides in vivo minimally invasive analysis-to a robotic arm of high accuracy, we demonstrate that images can be acquired from any surface by moving the laser probe above the surface. By equipping the robotic arm with a sensor, we are also able to both get the topography image of the sample surface and the molecular distribution, and then and plot back the molecular data, directly to the 3D topographical image without the need for image fusion. This is shown for the first time with the 3D topographic MS-based whole-body imaging of a mouse. Enabling fast in vivo MSI bridged to topography paves the way for surgical applications to excision margins.