Arequipa, situated in the arid Atacama Desert, is experiencing significant biodiversity loss due to unchecked urban growth. This study presents the design of a Botanical Garden to address this issue by serving as a conservation center for native flora. A baseline assessment was conducted to evaluate meteorological conditions, soil properties, and the quality of treated wastewater from the “La Escalerilla” plant. The analysis revealed a semi-arid climate with low precipitation and suitable soil conditions. A total of 685 plant species were identified and proposed for conservation within the garden, with a high proportion of endemic species. To protect the future plant species, a living fence composed of 700 individuals was installed, considering resilient species such as Molle serrano (Schinus molle), Cantuta (Cantua buxifolia), and Huaranguillo (Tephrosia cinerea), which were installed at an average height of 50 cm and have grown to an average of 80 cm after 8 months. This study demonstrates the feasibility of establishing a botanical garden in Arequipa’s arid environment and serves as a model for future botanical garden projects in arid regions at the national and regional levels, providing a foundation for natural landscapes in urban areas.