Abstract: Milkvetch (Astragalus membranaceus) is a staple herbal medicine in China. Few studies have investigated the nutrient requirements and fertilization management of organic milkvetch, and there are only a few reports on the proportioning and application of organic, mineral, and microbial fertilizers, which conform with organic cultivation. In this study, Mongolian milkvetch (Astragalus membranaceus var. mongholicus) was subjected to five treatments: no fertilizer (CK), chemical fertilizer (C), organic fertilizer (O), organic fertilizer + mineral fertilizer (OM), and organic fertilizer + mineral fertilizer + microbial fertilizer (OMD). The effects of different fertilizer treatments on the absorption, accumulation, and allocation of nine mineral nutrients (nitrogen, phosphorus, potassium, calcium, magnesium, iron, manganese, copper, and zinc) were systematically studied in the organs of organic Mongolian milkvetch. The results showed that the contents of nine mineral elements in various organs of Mongolian milkvetch varied with different fertilizer treatments. The accumulation of various elements in the roots of Mongolian milkvetch showed a gradually increasing trend, and the elements in the stems and leaves showed a dynamic trend, increasing at first and then decreasing. The application of chemical fertilizer effectively promoted the accumulation of iron, manganese, copper, and zinc in the stems and leaves of Mongolian milkvetch. Organic fertilizer combined with mineral and microbial fertilizers significantly promoted the accumulation of nitrogen, potassium, iron, manganese, copper, and zinc in the roots and promoted the accumulation of phosphorus in the stems and leaves. During the 180-day growth period after transplanting, organic fertilizer combined with mineral and microbial fertilizers performed best in all fertilization treatments. Compared with other treatments, the OMD treatment promoted the distribution of nine nutrients to the stems and leaves and provided more nutrients for growth. In summary, organic fertilizer combined with mineral and microbial fertilizers can effectively promote the accumulation and allocation of mineral nutrients in Mongolian milkvetch. This may represent the physiological basis for high yield and high-quality organic Mongolian milkvetch. However, the physiological mechanisms need further study.