Biochar is a carbon-rich material used to increase the fertility of the soil and improve its properties. It is produced through a process called pyrolysis which determines its stability. Biochar produced at low temperatures is known to have a lower half-life compared to those produced at higher temperatures. In this study, we investigated the effect of different clay co-amendments on biochar stability as measured through microbial respiration (cumulative CO2 production during the first month of incubation in soils). The effect on microbial enumeration, activity, and diversity was also assayed. We hypothesized that a) the biochar treated with inorganic clays increase biochar stability and reduce its degradation rate in calcareous sandy soils of Oman, and b) based on the available literature, allophane clays would be the most effective biochar additive for this purpose. Local clays were also tested as a sustainable alternative to Allophane and Ferrihydrite synthetic clays and were separated from the Al Khoud dam sediment after flocculation with Fe, Mg, Ca and HCl. Biochar clay homogenous mixtures were achieved in stirred suspensions at different doses (0, 0.032, 0.064, 0.128, 0.256, and 0.512) % by mass. Biochar that was obtained from date palm leaves was pyrolyzed at 450 °C and applied to the soil at 2.5% by weight. The results showed that biochar increased the soil microbial respiration rate, and the addition of different clays to biochar showed a stabilization effect bringing respiration rates closer to unamended soils. In general, the clays significantly reduced the average respiration rate except for soil biochar with local clays coated with calcium (SB-cCa) and soil biochar with local clays treated with hydrochloric acid (SB-cHCl) treatments. Moreover, ferrihydrite (Fh) at the maximum tested dosage (0.5%) was the most effective treatment to achieve this effect. The reduction in respiration rate was not reflected in a reduction in bacterial enumeration. The 16S rRNA prokaryotic community taxonomic diversity characterization showed more diversity in control soil compared with treated soils with 2.5% biochar and 0.512% clays and revealed a decreased abundance of archaea in samples amended with biochar and clays, with an increase in the dominance of firmicutes, especially in SB-cHCl treated samples. The differences in Shannon and Evenness diversity indexes for total operational taxonomic units (OTUs) between control soil and soil amended with biochar and clays were small, while for the class reduced compared with control soil. The addition of both locally sourced natural clays and synthetic clays caused a strong increase in the flavobacteriia class. The pH of biochar amendments appears to be driving the abundance of actinomycetia and betaproteobacteria. These findings highlight the potential of biochar and clays as effective soil management strategies for enhancing biochar stability and the long-term effect on carbon sequestration and other soil features offering a sustainable solution for agriculture and ecosystem restoration in arid regions.