Management interventions in agroforestry systems can reconcile ecological and productive outcomes while serving as part of forest restoration strategies. However, current knowledge on these impacts is still limited and controversial. Here, we assessed the effects of management intensity on coffee production and ecological indicators in coffee agroforests, as well as their potential for landscape restoration. Specifically, we identified key management practices, assessed their effects on production and ecology, analyzed potential trade-offs, and compared agroforests with old-growth forests. We assessed 10 old agroforests (15–19 years), 7 young agroforests (5–6 years), and 3 old-growth forests in the Atlantic Forest. We identified management practices most associated with coffee production using Principal Component Analysis and assessed management effects through Multiple Linear Regression. Trade-offs were tested with Spearman’s correlations, and ecological differences among systems were analyzed with ANOVA and Kruskal–Wallis tests. Higher management intensity—primarily through pruning, weeding, and natural fertilizers —significantly increased coffee production (p = 0.03) but did not impact ecological indicators. No trade-off was observed between production and ecological indicators. Overall, the management intensity and coffee production in the agroforestry were low. Old agroforests exhibited aboveground biomass levels comparable to old-growth forests. Despite relatively low coffee production, these agroforests enhance food security, income, and ecological benefits with minimal external inputs, offering a cost-effective strategy to landscape restoration. Our findings highlight that agroforestry with similar configurations but under low-intensity management can provide different benefits over time, depending on the combination of management practices.