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Protected areas (PAs) have been regarded as a critical strategy to protect natural forest (NF) and biodiversity. Estate‐crop expansion is an important driver of deforestation in Indonesia. Yet, little is known regarding the temporal dynamics of PA effectiveness in preventing estate‐crop expansion into NF. We employ Cox proportional hazard models and their extensions to characterize the dynamics of estate‐crop expansion into NF in Indonesia during 1996–2015. The results show that PA effectiveness in Sumatra decreased over time and became insignificant in 2012–2015. A multistate modeling analysis shows that hopping in land‐cover and land‐use change (LCLUC) trajectories with shrub and/or bare ground as intermediates has decreased PA effectiveness and facilitated the expansion. Preventing LCLUC trajectory hopping becomes crucial to biodiversity conservation because it tends to occur at lowland forest, diminishing natural habitat area and increasing NF isolation. [ABSTRACT FROM AUTHOR]