This paper presents a multiscale reactive flow model to simulate in-situ leaching of copper in heterogeneous porous microstructures. The introduced workflow combines fluid flow simulation with advection-diffusion-reaction simulation, both required to model reactive flow. The proposed workflow can include the fluid flow in resolved and unresolved pore structures and utilizes required parameters from molecular simulation (ionic diffusivity) and reaction databases (reaction rate parameters). The modeling approach is validated by comparing results to other open-source codes for a model calcite dissolution on acid injection. This model is applied to copper mining by leaching to analyze the reactive flow through a fractured digital rock model of a subsurface sample. Results are analyzed by tracking the concentration distribution along the pore space structure and calculating the outlet concentration of copper to conform the leaching path. Several sensitivity studies are performed to show the robustness of the modeling framework as well as to investigate the importance of each of these parameters on copper production. The complexity of the model is systematically increased from a single scale surface reaction model, to consider the influence of competitive bulk solution reactions, and finally to include flow through porous media to model multiscale reactive flow. This study shows that a multi-scale flow model with homogeneous bulk and heterogeneous surface reactions is required to accurately model copper leaching.