Epoxy‐based adhesive mortars are applied as bonding materials for the heavy‐duty fastener in buildings and constructions worldwide. The long‐term behavior of the adhesive mortars is a significant influencing factor on the sustained load and lifetime of bonded anchors. An adhesive mortar is a heterogeneous material consisting of resin and fillers. For the analysis of the long‐term performance of the bonded anchor, it is fundamental to understand the long‐term behavior of the bonding material on the microscale. This contribution presents a novel prediction approach for the long‐term load capacity of the epoxy‐based bonded anchor by using nanoindentation and FE‐simulation. The long‐term mechanical properties of the adhesive mortar were measured by using the precise nanoindentation technology on the micro level for the investigation of: (a) the loading rate effect on the load behavior of the resin, (b) the heterogeneous mechanical phases of the mortar, (c) the aging of the microstructures, and (d) the long‐term load behavior of the components of the mortar. Based on the experimental nanoindentation results, the numerical long‐term time‐independent material parameters were characterized in a concrete model by means of stochastic simulation. For analysis of the imperfection effect of a real bonded anchor, the nanoindentation was employed on the micro level to investigate the error load transfer on the interface between mortar and concrete drillhole without drill‐hole cleaning. On the macro level, the macroscale defects of an installed bonded anchor were found by using the computer tomography. It is demonstrated that the FE‐model based on the nanoindentation results can correctly predict the long‐term performances of a bonded anchorage system.