Laser-ablation inductively-coupled plasma tandem mass-spectrometry (LA-ICP-MS/MS) allows for rapid and interference free analyses of Rb and Sr isotopes, permitting in-situ Rb–Sr dating of minerals. However, the general lack of matrix matched reference materials remains one of its main obstacles, affecting both precision and accuracy. This study systematically investigates the impact of matrix effects and down-hole fractionation (DHF) on the in-situ Rb–Sr ages of an igneous phlogopite mineral (MDC) analysed by an ICP-MS/MS using two different LA systems: (i) a RESOlution ArF (193nm) excimer and (ii) a NWR (213nm) Nd-YAG laser system. A phlogopite reference material (Mica-Mg), originating from the same location as the MDC, was prepared as a pressed nano-powder pellet (NP) and used in this study as a primary reference material. The results revealed that the accuracy of the Rb–Sr ages is typically within about 3% (for 70% of analysed samples), but occasionally higher errors ranging between 4 to 8% were observed (ca. 30% of cases). We hypothesize that the above bias and uncertainty in the Rb–Sr ages are related to matrix effects between Mica-Mg-NP and MDC, due to their specific ablation characteristics and different physical properties. In addition, the elemental fractionation effects observed in this study for 87Rb/86Sr are also dependent on laser wavelength (i.e., 193nm vs. 213nm). Hence, developing an improved nano-powder reference material, or a mineral or glass with better matrix matching to natural phlogopite minerals would be desirable to further improve the accuracy of in-situ Rb–Sr dating. Currently, regular monitoring of secondary and matrix-matched reference minerals such as the MDC phlogopite can be used to assess and evaluate the accuracy of in-situ Rb–Sr dating of phlogopite, yielding ages within accuracy of ca. 3% or better.