Biotechnology has had a major effect on improving crude oil displacement to increase petroleum production. The role of biopolymers and bio cells for selective plugging of production zones through biofilm formation has been defined. The ability of microorganisms to improve the volumetric sweep efficiency and increase oil recovery by plugging off high-permeability layers and diverting injection fluid to lower-permeability was studied through experimental tests followed by multiple simulations. The main goal of this research was to examine the selective plugging effect of hydrophobic bacteria cell on secondary oil recovery performance. In the experimental section, water and aqua solution of purified Acinetobacter strain RAG-1 were injected into an oil-saturated heterogeneous micromodel porous media. Pure water injection could expel oil by 41%, while bacterial solution injection resulted in higher oil recovery efficiency; i.e., 59%. In the simulation section, a smaller part of the heterogeneous geometry was employed as a computational domain. A numerical model was developed using coupled Cahn–Hilliard phase-field method and Navier–Stokes equations, solved by a finite element solver. In the non-plugging model, approximately 50% of the matrix oil is recovered through water injection. Seven different models, which have different plugging distributions, were constructed to evaluate the influences of selective plugging mechanism on the flow patterns. Each plugging module represents a physical phenomenon which can resist the displacing phase flow in pores, throats, and walls during Microbial-Enhanced Oil Recovery (MEOR). After plugging of the main diameter route, displacing phase inevitably exit from sidelong routes located on the top and bottom of the matrix. Our results indicate that the number of plugs occurring in the medium could significantly affect the breakthrough time. It was also observed that increasing the number of plugging modules may not necessarily lead to higher ultimate oil recovery. Furthermore, it was shown that adjacent plugs to the inlet caused flow patterns similar to the non-plugging model, and higher oil recovery factor than the models with farther plugs from the inlet. The obtained results illustrated that the fluids distribution at the pore-scale and the ultimate oil recovery are strongly dependent on the plugging distribution.