Background: Denture base materials are subjected to sorption, a process of absorption and adsorption of liquids depending on the environmental conditions, also their fitting surface is subjected to microbial adhesion due to surface irregularities. Soft silicon liners are usually used with removable appliances to decrease load concentration on the hard and soft tissues. Silicon liners also undergo fluid sorption and microbial adhesion. Aim: This study was carried out to assess the effect of standardizing the oral hygiene conditions on the microbial load difference between conventional acrylic denture bases and silicon soft relining material (Mucopren soft) used to reline mandibular complete dentures in atrophied mandibles. Methods: Conventional complete dentures were constructed for 25 patients with flat atrophic mandibular ridges to be used for two weeks, salivary swabs were collected to evaluate oral flora attached on the fitting surface of the denture base and the buccal vestibule, soft liner was applied for all patients mandibular denture surfaces and the same approach was repeated after two weeks of the liner use. Results: Microbial load was found to be significantly higher in the fitting surfaces of the silicon soft liner, than in the conventional acrylic base fitting surfaces. Conclusion: Even under controlled oral conditions, Mucopren soft silicon liner incorporates greater microbial load than acrylic material thus, subjecting patients to numerous infections.