Climate-smart practices are actions that can be implemented without affecting agricultural activities and that can promote these activities, generating direct and indirect benefits in ecosystem services provision and increasing agricultural productivity and private income. The present study evaluated the effect of three climate-smart actions (establishment of isolated trees, recovery of riparian vegetation, and implementation of live fences) on increased functional landscape connectivity and carbon storage. Three scenarios with rates of participation ranging from 5 to 100% were tested in two watersheds with different degrees of conservation and a high priority for national food production in Mexico. The main results suggest climate-smart practices positively impact landscape connectivity and carbon sequestration. However, the improvement in landscape connectivity mainly benefits species of short displacement (50–100 m), and the increase in carbon storage is directly linear to the area implemented in these practices. Also, the effectiveness of the modeled actions depends on the landscape structure, which was implemented with the highest benefits in watersheds with intense agricultural activity. The findings can support decision-makers in selecting the best strategies to increase landscape connectivity and carbon sequestration in productive landscapes.