Phenological parameters extracted from time series (TS) of spectral indices are essential to characterizing crops. However, the lack of data in the TS can affect their accuracy. The Copernicus Land Monitoring Service (CLMS) provides these parameters and their temporal quality. This paper evaluates the impact of missing vegetation index data on phenological parameters, namely, SOS, EOS, and MAX, for extensive arable crop between 2018 and 2023. The TSGenerator package was developed to download, process, and analyze the data. We used 252 images from the BIOPAR-VI module, 6 phenology parameters, and 2025 plots of barley and maize in Monegros and Zaidín, Spain. In barley, SOS and MAX showed 42.9% and 40.9% of missing data, while in maize, SOS and EOS showed 36.6% and 41.0%. The correlation between the Copernicus VPP quality parameter and the proposed one was r = 0.89 for barley and r = 0.74 for maize. This study advances the understanding of the effect of missing data on SOS, EOS, and MAX.