Bio-grouting is an environmentallly friendly, sustainable, and low-cost ground improvement technique, which mainly utilizes microbial-induced carbonate precipitation. Previous large-scale applications of MICP have encountered practical difficulties including bio-clogging, which resulted in a limited zone of cemented soil around injection points. The research presented in this paper focuses on evaluating the feasibility of cementing a limited soil zone surrounding permeable piles using MICP bio-grouting to improve the mechanical response of permeable piles under axial pull-out loading. Two instrumented pervious concrete piles (test units), one with and one without MICP bio-grouting, were subjected to pull-out loading at the Soil-Structure Interaction Facility at Lehigh University. The pervious concrete pile served as an injection point during the MICP bio-grouting. The mechanical responses of the test units and surrounding soil were analyzed, along with shear wave (S-wave) velocities, moisture, and CaCO3 contents of the surrounding soil. The results presented in this paper demonstrate that the limited MICP-improved zone, extending a radial distance of approximately 102 mm around pervious concrete piles, improved the load–displacement response, load transfer, and pile capacity under pull-out loading. The ratios between ultimate loads of the test units with and without MICP bio-grouting were 4.2. The average shaft resistance along the pile with MICP bio-grouting was up to 2.8 times higher than that of the pile without bio-grouting.