The impact of long-term exposure to Sr2+ (LTE, four doses, 43.5 mg Sr2+ per pot, with a total of 174 mg Sr2+ per pot during the entire period of cultivation) and short-term exposure to Sr2+ (STE, one dose, 870 mg Sr2+ per pot four days before harvest) on the content of phytoestrogens and allantoin in soybeans were compared. Sr2+ accumulation, the effect on the concentration of macroelements, and basic physiology were also analyzed. LTE reduced the content of malonyldaidzin and malonylgenistin in the roots (58% and 50% compared to the control, respectively). STE increased the amount of all isoflavones in the stem and genistein in the leaves and decreased the content of malonyldaidzin and malonylgenistin in the leaves (55% and 48% compared to the control, respectively) and roots (69% and 62% of the control, respectively) as well as genistein and coumestrol in the roots (both 50% compared to the control). Sr2+ presence stimulated the accumulation of allantoin in the roots (three-fold higher than in the control), but only STE had similar effects on the shoots. In contrast to LTE, Sr2+ was transported extensively from the roots to the leaves under STE. In comparison to the control, LTE resulted in an increase in the Ca content in the stem by 36%, whereas Ca2+ accumulation in the leaves, stems, and roots increased by 60%, 80%, and 36%, respectively, under STE. Additionally, a significant accumulation of K was found only in the roots of the LTE group. The chlorophyll content did not differ between the treatments. Overall, the production of phytoestrogens and Sr accumulation were affected by both the applied dose and the duration of exposure to Sr.