The formation damage (FD) caused by the invasion of drilling fluid severely affects reservoir performance during production. Most of the published research studies which address this type of FD have been carried out at the core or field scale. Thus, the main aim of the paper is to investigate the pore-scale mechanisms of FD induced by drilling fluids and their control with silica nanoparticles (NPs) using a microfluidic approach. The proper identification of the mechanisms of FD can lead to the proper selection of NP type and concentration as well as a suitable method to remediate FD. The micromodel was designed in a way to closely simulate the cross-flow at the wellbore surface. A water-based drilling fluid was prepared at low- and high-pH values of 9 and 10.7, respectively. The drilling fluid was augmented with silica NPs at different concentrations to study its impact on FD remediation. The drilling fluid was injected into an initially oil-saturated micromodel. Thereafter hydrochloric acid was injected as a cleanup fluid. Lastly, oil was flowed back into the micromodel from the opposite side to simulate the back production. The study was complemented with cutting transport simulation and measurement of filtration and bulk rheological properties of the drilling fluid. The pore-scale observations reveal three types of FD associated with the drilling fluid invasion: (1) primary, (2) secondary, and (3) tertiary. The type of FD was found to be dependent on the mud pH, necessitating the use of different NP concentrations. Primary FD is caused immediately after drilling fluid invasion into the porous medium and includes the internal mudcake deposition (with both low- and high-pH muds) and water blockage (mainly with high-pH mud). After acid cleaning and oil flow-back, the secondary FD is induced which includes in situ acid-in-oil emulsion formation within the pore structure of the mudcake (with both low- and high-pH muds) as well as on the micromodel surface (mainly with high-pH mud). The tertiary FD originates from the relocation and trapping of mobile emulsions. It was also found that, in the case of primary FD, the NPs reduce the penetration depth of the drilling fluid into the micromodel through external (or face) and internal plugging mechanisms. Moreover, NPs eliminate the water blockage by reducing the mud infiltrate volume as well as reducing the IFT. For the case of secondary FD, NPs do not allow the formation of acid-in-oil emulsions within the internal mudcake due to increased drilling fluid stability. In addition to reducing the infiltrate volume, NPs prevent the formation of emulsions on the pore surface by altering the wettability of the micromodel to a more water-wetting state. By reducing the primary and secondary FD, the tertiary FD is eliminated too. The findings from the micromodel experiments highlight the importance of optimizing the NP concentration based on both attaining an efficient cutting transport in the well and ensuring low mud invasion into the porous medium.