Biogeomechanics is a novel and resourceful approach to assessing the impact of biological processes on the mechanical properties and behavior of rocks and rock-like materials. However, there is still a lack of knowledge on how far an in-situ bacterial growth can invade a reservoir rock with time and what its long-term impacts at nano- to micro-scale are in the invaded reservoir. This study uses non-destructive methods to investigate time-dependent nano-scale extent of biogeomechanical and morphological alterations in carbonate rocks due to microbial invasion. We conducted a microbial treatment of carbonate rock samples using a distinct microbial solution over a period of 30, 60, 90, and 120 days at a temperature of 42°C. Subsequently, the sub-core scale properties of untreated and post-treatment carbonate rocks were measured using Atomic Force Microscope (AFM) and Scanning Electron Microscope (SEM) to assess the changes in surface roughness and pore structure. Finally, we compared the untreated and microbially treated samples and assessed the implications for mechanical properties to better understand how microbial invasion could impact carbonate rocks. The results suggest that distinct microbes can continue to invade and alter the formation over time causing dissolution and disintegration of the rock matrix, which may yield a reduction in the mechanical integrity of the microbially impacted carbonate rock.