Resilience has been growing in importance as a perspective for governing social-ecological systems. The aim of this paper is first to analyze a well-studied human dominated agroecosystem using five existing key heuristics of the resilience perspective and second to discuss the consequences of using this resilience perspective for the future management of similar human dominated agroecosystems. The human dominated agroecosystem is located in the Dutch Northern Frisian Woodlands where cooperatives of dairy farmers have been attempting to organize a transition toward more viable and environmental friendly agrosystems. A mobilizing element in the cooperatives was the ability of some dairy farmers to obtain high herbage and milk yield production with limited nitrogen fertilizer input. A set of reinforcing measures was hypothesized to rebalance nitrogen flows and to set a new equilibrium. A dynamic farm model was used to evaluate the long-term effects of reinforcing measures on soil organic matter content, which was considered the key indicator of an alternative system state. Simulations show that no alternative stable state for soil organic matter exists within a plausible range of fertilizer applications. The observed differences in soil organic matter content and nutrient use efficiency probably represent a time lag of long-term nonequilibrium system development. The resilience perspective proved to be especially insightful in addressing interacting long-term developments expressed in the panarchy. Panarchy created a heterogeneity of resources in the landscape providing local landscape-embedded opportunities for high N-efficiencies. Stopping the practice of grassland renewal will allow this ecological landscape embedded system to mature. In contrast, modern conventional dairy farms shortcut the adaptive cycle by frequent grassland renewals, resulting in high resilience and adaptability. This comes at the cost of long-term accumulated ecological capital of soil organic matter and transformability, thus reinforcing the incremental adaptation trap. Analysis of such a human dominated agroecosystem reveals that rather than alternative states, an alternative set of relationships within a multiscale setting applies, indicating the importance for embedding panarchy in the analysis of sustainable development goals in agroecosystems.