Background: PET imaging of 90Y-microspheres distribution following radioembolisation is a challenging task due to the count-starved statistics from the low branching ratio producing e+/e- pairs during 90Y decay. The recent PET systems using silicon photo-multipliers technology has shown better 90Y image quality compared to photo-multiplier tubes. The aim of the present study was to quantitatively evaluate the impact of 90Y imaging conditions and reconstruction parameters on the dosimetry calculations using a digital photon counting PET.Methods: Quantitative PET and dosimetry accuracy were evaluated using two uniform cylindrical phantoms specific for PET calibration validation. A body phantom with an 9:1 hot sphere-to-background ratio was scanned at different activity concentrations of 90Y. Reconstructions were performed using OSEM algorithm with varying parameters. Time-of-flight and point-spread function modellings were included in all reconstructions. Absorbed dose calculations were carried out using Voxel S-Values convolution and were compared to reference Monte Carlo simulations. Dose-volume histograms and root-mean-square deviations were used to evaluate reconstruction parameter sets. Thanks to listmode data, datasets for phantoms and patients were rebinned into varying lengths of time to assess the influence of acquisition duration on the calculation of absorbed dose. Results: A 2 mm full width at half maximum post-reconstruction Gaussian filter size can be used for image reconstruction, keeping the same accuracy as when no filter is applied for dosimetry purposes and reducing noise. Larger filter sizes should not be used. An acquisition duration of more than 10 min/bed reduces image noise but has no significant impact in the quantification of phantom and patient data for the digital photon counting PET. 3 iterations with 10 subsets was found suitable for large spheres whereas 1 iteration with 30 subsets could improve dosimetry for smaller spheres. Conclusion: The choice of iterations and subsets combination depends on the size of the spheres. However, one should be careful on this choice, depending on the imaging conditions and setup. This study can be useful in this choice for future studies for more accurate 90Y post-dosimetry using a digital photon counting PET.