Understanding aging in seeds is vital for conservation and long-term preservation. This study examined the physiological and lipid characteristics of three chia varieties (WN, MNI, MNII) using conventional and biophysical methods to establish correlations and explore aging mechanisms. Variables assessed included thousand seed weight, moisture content (MC), and germination parameters, such as normal germination power (NGP), hypocotyl and radicle length, vigor, viability, as well as lipid characteristics, and thermal parameters. Physiological differences were prominent, especially in the MNII, with longer mean germination times (MGT = 2.11 d) and reduced NGP (63.24%). The WN variety exhibited superior germination (NGP = 95.9%), while MNI had an NGP of 93.2% and the highest vigor. Lipid analysis revealed significant differences, particularly in free fatty acid content (FFA). The oxidative status and tocopherol content were evaluated, with high germination in WN being associated with the combination of tocopherol isomers. The thermal analysis highlighted the predictive potential of ΔH for seed health and viability. Spectral analysis distinguished nutlets and oils, showcasing unique vibrational patterns. The correlation analysis revealed significant relationships crucial for conservation. MGT showed positive correlations with moisture content, electrical conductivity, and FFA, but negative correlations with germinated nutlets (GN) and normal seedlings (NS). MC positively correlated with FFA, abnormal seedlings (AS), and deteriorated nutlets, yet negatively correlated with GN and NS. Electrical conductivity emerged as a germination indicator, positively correlating with FFA and deteriorated nutlets, and negatively with GN and NS. δ-tocopherol content positively correlated with successful germination and NS, but negatively with AS. Thus, this research provides relevant knowledge on the conservation of chia nutlets by offering information on seed deterioration markers that can be obtained by FT-IR and DSC. This is particularly valuable for studying germplasm with a limited sample size, common in gene banks. Display omitted •Physiological, biochemical, and biophysical changes were compared for different chia genotypes.•All physiological properties exhibited suboptimal values for the MNII cultivar.•Free fatty acids proved to be a reliable indicator of nutlets deterioration.•The fusion energy determined by DSC correlated with the degree of deterioration.•PCA analysis of FT-IR separated cultivars with different physiological performances.