The frequent use of plant-based products to promote health leads to the search for scientific information related to efficacy and safety of those products for human consumption. Two alfalfa-derived products (ADP), freeze-dried juice (FDJ) and dehydrated powder (DP), from alfalfa harvested in Mexico, are being developed as new possible nutraceuticals. To the best of our knowledge, any study reports the real composition of such products used to prepare instant beverages in what concerns isoflavone contents. Seven isoflavones (glycitein, formononetin, biochanin A, daidzein, genistein, daidzin and genistin) were assessed by HPLC-DAD analysis as well as its variation in five different batches of these products. Different solvents were tested in order to choose the best one to extract isoflavones. The results showed the presence of daidzein, genistein, genistin and daidzin in most samples while glycitein, formononetin and biochanin A were not detected. Significant differences between isoflavone contents were found with different solvent systems. Water was the best option to extract daidzein (0.40–1.08 mg per unit and 1.30–4.90 mg per unit for DP and FDJ, respectively) whereas the water–methanol–formic acid mixture was efficient to extract genistein (0.19–0.43 mg per unit and 0.15–0.72 mg per unit for DP and FDJ, respectively). In all cases, the total isoflavone content was higher in freeze-dried juices than in dehydrated powders. Genistein and daidzein were the more abundant isoflavones quantified. Further physiological and nutritional studies are needed to complete the validation of effectiveness and safety of these products.