Food supply chains in the southern border counties of Texas and New Mexico face persistent disruptions driven by environmental, infrastructural, socioeconomic, and policy-related stressors. Understanding these challenges is crucial for informing coordinated efforts to enhance regional food systems. We conducted a scoping review to identify and synthesize evidence on challenges and barriers affecting food supply chains in the region. Peer-reviewed articles and grey literature published between 2014 and 2024 were searched and appraised using the AACODS framework. Nine sources met the inclusion criteria and were analyzed to characterize cross-sectoral challenges spanning production, aggregation, distribution, and retail systems. Findings reveal a set of interconnected barriers shaping regional food supply chains. Environmental stressors, including drought, aquifer depletion, extreme heat, and conflicts over water governance, limit agricultural productivity and increase reliance on external suppliers. Infrastructure gaps, particularly shortages of aggregation hubs, cold storage facilities, and transportation networks, further constrain efficient movement of goods. Cross-border dependencies, such as inspection delays, regulatory shifts, and policy uncertainties at U.S.-Mexico ports of entry, exacerbate systemwide vulnerabilities. Finally, retail-access inequities in rural colonias, where many communities rely on small outlets with limited refrigeration and constrained inventory capacity, interact with structural affordability barriers, limiting the availability and variety of fresh, perishable foods. Across sectors, food supply chains in the Texas–New Mexico border region are shaped by cascading challenges that span environmental stressors, infrastructure deficits, and cross-border policy volatility. Upstream disruptions in water governance, labor stability, and aggregation capacity amplify transportation costs and downstream retail constraints. These findings identify actionable priorities for regional decision-makers, including strategic investment in cold-chain and aggregation infrastructure, coordinated binational port and inspection processes to reduce spoilage risk, and workforce-stabilization policies that support small- and midscale producers.