Platelet polyphosphate (polyP) can be conveniently quantified by a recent methodological breakthrough using 4′,6-diamidino-2-phenylindole (DAPI). However, the preservation of these biological samples has not yet been standardized. In a preliminary study, possible protocols were screened, and passed protocols were further tested in this study. Pure-platelet-rich plasma (P-PRP) samples and washed platelet suspensions were prepared using blood obtained from non-smoking, healthy male donors and fixed with ThromboFix for 24 h at 4 °C. Mass polyP levels were determined using a fluorometer at wavelengths of 425 and 525 nm. Platelet polyP levels were normalized to platelet counts. Statistical analyses were performed using non-parametric tests. In platelet suspension maintained in fixed conditions at 4 °C (control), platelet polyP levels significantly decreased by 20% at and after 7 days. In contrast, platelet polyP levels in both P-PRP and washed platelet suspensions were maintained without significant reduction for up to 6 weeks by removing ThromboFix after fixation and subsequent freezing in pure water at −80 °C. Owing to the low specificity of DAPI binding and the wavelengths used, fluorometric polyP quantification is often interfered with. Our validated protocols will enable long-term preservation and high-throughput polyP quantification and could be applied to relatively large cohort studies.