The phenol-sulfuric acid (PSA) method is a widely used colorimetric method for determining the total saccharides. Microplate-based PSA methods have been developed to handle a large number of samples and reduce the use of hazardous chemicals. However, the optimal procedures and measurement conditions for this method have not yet been fully established. To address this gap, we investigated the optimal procedure for microplate-based PSA. In addition to glucose (Glc), two types of cellulose nanofibers (CNFs) were also evaluated as they are a new type of nanomaterial, and a technique to quantify the concentration of CNFs is required in their safety assessment. The results showed that the thermal reaction with sulfuric acid before the addition of phenol resulted in a higher coloration than was shown after the addition of phenol. Furthermore, the longer the resting time after shaking with phenol, the greater the coloration and the smaller the variation, with a resting time of 60 min or longer being optimal. This research provides valuable insights into improving the reliability and efficiency of the PSA method, which can facilitate the analysis of saccharides and other substances in a range of applications.