Organic germanium (Ge) compounds show vital beneficial effects for our health and are widely used as medical applications and dietary supplements. Inorganic Ge can be absorbed by plants and further accumulated and transformed into organic Ge compounds in plant tissues, which can be further consumed as Ge-rich foods. Meantime, the presence of Ge can improve the physiological functions of plants such as the salt tolerance and the peroxidase activities in leaves. Therefore, improving the Ge content of Ge-rich plants by fertilizing exogenous inorganic Ge is of important and an efficient way to obtain more organic germanium. Garlic is one of the natural Ge-rich plants and possesses prodigious medicinal and nutraceutical properties. The main edible parts of garlic include bulb, scape and seedling in China. However, the effects of exogenous Ge on the Ge accumulation and nutritional qualities of garlic are not apparent, and the suitable applying concentrations and frequencies are also poorly known. Here, using garlic cultivar G024 and GeO₂ as exogenous Ge, two experiments were performed to reveal the effects of exogenous Ge on garlic. Besides, a third experiment that brings in the factor of effective microorganisms (EM) inoculation was also conducted to evaluate the combined effects of exogenous Ge and EM application on garlic seedlings. Results showed that foliar spraying 6–72 mg/L GeO₂ solutions significantly affects the Ge accumulation and distribution in garlic plants; foliar spraying 9–12 mg/L GeO₂ at the bolting period is appropriate for producing the Ge-rich garlic scapes and bulbs; soil supplying 100 mg GeO₂ together with EM inoculation are suitable for obtaining Ge-rich garlic seedlings. The present study provided useful information for the field production of Ge-rich garlic.