The massive arrival of Sargassum biomass on the Caribbean coast is a potential raw material source that needs an assessment of its quality and preservation state. Thus, the present study aimed to investigate how pelagic Sargassum changes its chemical composition due to sample transportation, morphotype (S. natans I, S. natans VIII, and S. fluitans III), and exposure to open-air conditions during two months of outdoor conditions using Fourier Transform Infra-Red (IR) spectroscopy and chemometric analysis. The results demonstrate that cold transportation to the lab before flash-freezing caused sample degradation, characterized by mannitol consumption and the formation of anaerobic metabolism products. Multivariate analyses showed that the IR spectral zone with differences between S. natans and S. fluitans were in the same IR spectral regions related to sample degradation. In the two flash-freezing treatments, S. fluitans had the highest IR peak absorbance of mannitol and a lower absorbance for the carboxylic acids IR peak. Between S. natans morphotypes, S. natans I had the highest modification caused by the cold transportation to the lab. The decomposition under prolonged time (up to eight weeks) in open-air conditions demonstrated an increased absorbance on the IR bands of carboxylic acids in the first four weeks. In the sixth and eighth weeks, the IR signals of calcium carbonate increased more than those from organic matter. This study provides a better understanding of the importance of preserving the collected samples and how the decomposition dynamics of Sargassum species may impact the extraction of key compounds, e.g., alginate and mannitol.