In recent years, nanoparticles have gained significant importance due to their unique properties, such as pharmacological, electrical, optical, and magnetic abilities, contributing to the growth of the science and technology sector. Particular naturally derived biomolecules with beneficial effects on menopause disorder have been the subject of studies of pharmaceutical formulation to obtain alternative pharmaceutical forms with increased bioavailability and without side effects, as in nanostructured lipid carriers (NLCs) loaded with such active ingredients. In the present study, one stage of a broader project, we have performed pharmacotoxicology studies for six combinatory innovative nanocapsule pharmaceutical forms containing active natural biomolecules before considering them as oral formulas for (1) in vitro toxicity studies on culture cells and (2) in vivo preclinical studies on a surgically induced menopause model of Wistar female rats, and the influence of the NLCs on key biochemical parameters: lipid profile (TG, Chol, HDL), glycemic markers (Gli), bone markers (Pac, Palc, Ca, phosphorus), renal markers (Crea, urea, URAC), inflammation (TNF), oxidative stress (GSH, MDA), and estrogen–progesterone hormonal profile. The micronucleus test did not reveal the genotoxicity of the tested compounds; the menopause model showed no significant safety concerns for the six tested formulas evaluated using the blood biochemical parameters; and the results showed the potential hypoglycemic, hypolipidemic, hypouricemic, and antioxidant potential of one of the tested formulas containing nano diosgenin and glycyrrhizic acid.