Potential time lags between human-mediated disturbances and the subsequent responses of ecosystems are critical for planning and implementing conservation and restoration actions. In this context, decoupling between the temporal trajectories of ecosystems structure and functions is particularly critical. Here, we stand out the need to differentiate the temporal trajectories of ecosystem structure and functions to be considered in ecological restoration programs. In cases when ecosystem functions persist after the degradation of the ecosystem structure, and when functions do not recover at the same rate as structure, some kind of ecosystem functioning credits or debts can occur. In other situations, an ongoing loss of the ecosystem function can occur even in the absence of further disturbance. Ecosystem restoration outcomes could be optimized in regions with ecosystem functioning credit, since mitigating the decline in functioning will be more efficient than recovering functions in highly degraded conditions. Ecological restoration programs should not only focus on structure-derived indicators but they should also consider the dynamics of ecosystem functions to guide land-planning decision-making.