This study explores the capacity of grout injection as a compatible solution for repairing cracks and preventing water ingress in the damaged masonry walls of the Wupatki Pueblo archaeological site (Arizona). This historical site, built primarily with sandstone units and earthen mortar joints, faces accelerated degradation forms, such as cracks and voids, due to harsh environmental conditions that threaten its structural integrity and long-term durability. In this context, three trial zones were selected for the injection process employing a compatible clay-based grout specifically designed using mainly local soil. The grout mixture was designed to achieve adequate fluidity, strength and durability. The composition of the injected grout was subsequently validated by testing its fresh and hardened properties in terms of fluidity and mechanical strength. Overall, the injection of clay-based grouts proved to be a suitable intervention for consolidating the masonry walls of the Wupatki Pueblo. Specifically, the grout mixture exhibited fresh-state properties appropriate for crack injection and adequate compressive strength. In addition, the injection interventions did not disturb the architectural aesthetic of the masonry, which makes this technique suitable for integration in the site’s conservation plan.