Sea buckthorn (Hippophae rhamnoides L.) is a thorny, nitrogen-fixing shrub native to Europe and Asia. Known as the “vitamin tree,” sea buckthorn is an important fruit resource for the Mongolian people. However, comparative studies on the antioxidant activity of wild sea buckthorn in Mongolia are still lacking. Therefore, the objective of this research was to determine the optimal extraction method to maximize its functional properties and to evaluate the antioxidant and antimicrobial activities of wild Mongolian sea buckthorn berry extracts. The wild Mongolian berries were extracted using hot water, 70% methanol, and 70% ethanol through three different extraction methods: homogenizer-assisted extraction, ultrasonication-assisted extraction, and Soxhlet extraction. The antioxidant and antimicrobial activities of the sea buckthorn extracts were assessed by measuring total phenolic content (TPC), total flavonoid content (TFC), DPPH free radical scavenging activity, ferric reducing antioxidant power (FRAP), reducing power, nitric oxide (NO) radical scavenging capacity, nitrite scavenging activity, and the diameters of inhibition zones against foodborne pathogens. The DPPH free radical scavenging capacity and FRAP of the sea buckthorn berries extracted using Soxhlet with 70% ethanol were 57.36% and 1.035 mg FSE/g, respectively. The Soxhlet 70% ethanol extract also exhibited the highest reducing power (1.961), NO radical scavenging ability (64.7%), and nitrite scavenging ability (62.4%) among the tested samples. The hot water, 70% methanol, and 70% ethanol extracts exhibited concentration-dependent antimicrobial activity. The homogenizer-assisted 70% ethanol extract formed a clear inhibition zone of 13 mm against Salmonella enteritidis.