Heavy metals contamination of agriculture soil is an important ecological problem. Rapid growth of industrial sector and lack of proper disposal system of industrial wastes heavily loaded our soil with toxic metals possessing serious threat to all form of life. Present study was carried out to explore the bioremediation potential of two heavy metals resistant bacterial strains (Bacillus aerius and Bacillus cereus) isolated from heavy metals polluted soils of Hayatabad industrial estate, Peshawar (HIEP) and Gadoon industrial estate, Swabi (GIES) of Khyber-Pukhtoonkhwa, Pakistan, by assessing the biochemical and molecular processes occurs in spinach crop grown in that soil. Elemental study of the soils indicated that concentration of heavy metals in target areas were significantly higher than control i.e. (Pb= 98.33 in Gadoon and 65.08 mg/kg in Hayatabad > 0.4 mg/kg in control soil), (Cr=102.66 in Gadoon and 30.56 in Hayatabad > 2.78 mg/kg in control soil), (Cu=25.66 in Gadoon and 12.4 mg/kg in Hayatabad > 1.35 mg/kg in control soil), (Mn=839.66 in Gadoon and 753.43 mg/kg in Hayatabad > 28.9mg/kg in control soil), (Zn=47.33 in Gadoon and 22.56 mg/kg in Hayatabad > 0.04mg/kg in control soil. Diverse statistical tools like cluster analysis (HC) and principal component analysis (PCA), along with geo-statistical approches such as single pollution load index (SPI), ecological risk factor (Er), enrichment factor (EF) and geoaccumulation index (I-geo) proved significant to moderate enrichment of heavy metals in the soil. Hence, this study indicates that the majority of toxic heavy metals contributed to soil pollution in the studied areas are coming from industrial and commercial activities. To explore the effect of heavy metals on lipid peroxidation in spinach associated with microbes (B. aerius and B. cereus) isolated from contaminated soils irrigated with industrial effluents of GIES and HIEP. The severity of the lipid peroxidation induced by heavy metals was determined by Thiobarbituric acid reactive substances (TBARS) contents, glycine betaine (GB), proline (Pro) contents, hydrogen per oxide (H2O2) contents, photosynthetic pigments (chlorophyll “a”, chlorophyll “b” and “carotenoids”, total soluble sugar (TSS), proteins (TP) contents, and cell viability (EC) estimation. Plants grown in heavy metals polluted soil showed significant reduction in chlorophyll “a”, chlorophyll “b”, carotenes, total soluble sugar and total proteins contents, whereas electrolyte contents, glycine betaine, proline, hydrogen peroxide and TBARS in terms of lipid peroxidation were increased. Seeds inoculated with microbes showed significant increase in photosynthetic pigments, total soluble sugar and proteins contents whereas cell leakage, glycine betaine contents, proline, hydrogen peroxide contents and TBARS, confirmed decrease in oxidative stress produced by heavy metals. Plant physiological and biochemical attributes like germination percentage, seedling vigor, total nitrogen and proteins contents, metallothionein contents, stomata morphology and antioxidative metabolism associated with heavy metals resistance microbes (B. aerius and B. cereus) showed that heavy metals pollution significantly decrease seed germination, plant growth and vigor, total nitrogen and proteins contents, whereas significantly high metallothionein (MTs) and antioxidants enzymes were noted. Conversely, B. aerius and B. cereus species alleviated heavy metals induced reduction in plant biomass and improved seed germination, total nitrogen and proteins contents, reduced metallothionein and antioxidative enzymes. Furthermore Stomata microstructural alterations were significantly revived by bacterial strains. Results further revealed that plants inoculated with heavy metals resistant bacterial strains were efficient in heavy metals removal from polluted soil as compared to non-inoculated plants. Furthermore both heavy metals resistant strains inoculated plants showed high tolerance index (TI) and low bio-accumulation factor (BF) by comparing with non-inoculated crop ensuring restricted flow of heavy metals to plant system. Reverse Transcription of expressed genes revealed the stress response of two gene families Myeloblastosis (Myb) and Zinc-figure protein genes (Zat-12) in plants grown in contaminated soils. There was very low expression of Myb and Zat-12 genes i.e. 26 and 20%) in GIES soil and 15.78 and 10% in HIEP soil in bio-primed plants, while in non-bio primed plants these values were 100% in GIES soil and 31 and 80% in HIEP soil. It is therefore recommended that plant augmented with heavy metals resistant strains not only regulates the expression of stress inducible genes but also play a major role in the remediation of heavy metals affected agriculture soil.