Ion counting with an electron multiplier (EM) is necessary when sputtered ions are used for in situ and precise isotopic abundance measurements (10−4$(1\sigma)$) on small sample volume (about 100 μm3 for pure silicon). Measurements were performed on silicon samples bombarded with Cs+ ions by extracting negative secondary monatomic Si− ions. Pulse-height distributions (PHD) and isotopic ratios were used as diagnostic tools for repeatability studies. Repeatability could be greatly improved by determining the optimal position of the impact area on the conversion dynode and by addressing each isotopic beam properly focused on this area (adaptive optics). A simplified model based on Poisson's laws was developed to fit PHDs and allowed us to calculate quantum detection efficiencies versus thresholds. EM isotopic discriminations were determined with the resulting semiempirical algorithm so as to reconstruct the lost information and get data independent of threshold setting. To reach consistent results, quasi-simultaneous arrivals (QSA) on the conversion dynode had to be assumed and modelled using direct ionisation yields Si−/ Cs+ at different collection efficiencies. The QSA corrected data fitted well on the terrestrial isotopic fractionation line. Dead time uncertainties and possible emission non-linear isotopic fractionation processes were examined. PHDs from other elements and polyatomic ions were also discussed.