In 2017, we introduced the OrbiSIMS instrument that features a dual analyser configuration with a time‐of‐flight (ToF) mass spectrometer (MS) and an Orbitrap MS, which confer advantages of speed and high‐performance mass spectrometry, respectively. The ability to combine the MS performance usually found in a state‐of‐the‐art proteomics and metabolomics MS with 3D imaging at the microscale and from nanolayers of <10 nm of material has proved popular in a broad field of application from organic electronics to drug discovery. There are now several instruments in operation around the world, and metrology is needed to help ensure repeatability and reproducibility of the intensity scale. We conduct a systematic study of two key parameters, the target potential, VT, and the collision cell pressure, P, in the transfer optics on the transmitted secondary ion intensities. We measure VT–P maps of the ions across the mass range for Ag as a representative of inorganic materials and two different organic materials, Irganox 1010 and NPB (N,N′‐Di[1‐naphthyl]‐N,N′‐diphenyl‐4,4′‐biphenyldiamine). The manufacturer's defaults for these values ensure very good transmission for a broad range of analyte classes. However, the maps reveal a sometimes complex behaviour and indicate the possibility for additional separation of ions based on their shape, labile nature and kinetics of formation. Guidance is provided on how to optimise these parameters for sensitivity for different material classes and also the need for optimisation to improve spectral repeatability and reproducibility.