Biochemical profiling of 90 linseed (Linum usitatissimum L.) varieties was done to have insights into their health benefits and nutritional properties. The analysis of fatty acid (FA) composition revealed 5 major FAs as α-linolenic acid (ALA), linoleic acid (LA), oleic acid (OA), palmitic acid (PA), and stearic acid (SA) ranging from 1.68% to 59.19%, 5.61–62.44%, 18.14–45.54%, 5.69–9.5%, and 3.94–10.29%, respectively. Secoisolariciresinol diglucoside (SDG) content varied significantly with a wide range of 0.02–3.60% in the seed with highest SDG content recorded so far as 3.60% in variety KL-226. Amino acid (AA) composition analysis revealed the variation in average amino acid content of essential amino acids (EAA) (His, Thr Val, Met, Trp, Phe, Ile, Leu, Lys) and non-essential amino acids (NEAA) (Asp, Glu, Ser, Gly, Arg, Ala, Tyr, Cys). Total NEAA content ranged from 3.24% to 23.69% while total EAA content ranged from 1.89% to 14.89%. Lipid heath indices such as atherogenicity index, thrombogenicity index, cholestrolemic index and peroxidisability index along with other fatty acid ratios such as n-6/n-3 ratio, UFA/SFA, PUFA/SFA were calculated to determine the stability of the varieties against auto-oxidation. It also revealed the positive effect of all varieties providing protection against atherosclerosis, coronary heart diseases, cancer and inflammatory diseases. Oleic desaturation ratio (ODR) and linoleic desaturation ratio (LDR) calculated to determine the desaturation efficiency of fatty acids, while protein efficiency ratio (PER) value calculated using amino acid composition determine the nutritional quality of protein. PER value ranged from 1.92 to 4.12 making all 90 varieties a good quality protein plant source. Principal component analysis revealed a significant variation between the fatty acid composition, amino acid composition and SDG content with a total variation of 69.95%. Hierarchical cluster analysis calculated using Pearson correlation coefficient revealed that 89 varieties are mostly similar except TL-99 variety.