X-ray microbeams are a potential, novel mode of radiation therapy and dosimetry methods are under development that require micrometric spatial precision. The microDiamond detector has the requisite resolution and is composed of diamond which is closely tissue-equivalent. The high density of diamond however perturbs of secondary electrons and Monte Carlo methods are needed to determine corrections to accurately measure clinical parameters. The PENELOPE Monte Carlo code has been used to calculate corrections for the output factor (OF) and peak-to-valley dose ratio (PVDR). A high-performance computing (HPC) system was found to be necessary and the calculation took 72 hours when performed on a cluster of 100 CPUs. The correction for the output factor was found to be 1.009±0.016 (2 s.d.). The correction factor for the peak-to-valley ratio was found to be 1.144±0.013 (2 s.d.) and was larger due to Compton scattering of the microbeam in the extracameral components of the detector, in particular the 300 micron bulk diamond crystal. It was found that considerable improvements in efficiency could be achieved without loss of precision by switching off electron transport for electrons that are generated far from the sensitive element of the detector.