Valorisation of agriculture waste namely rice straw (RS) for the recovery of value-added products such as high purity silica and biogas has gained tremendous research interest. Presence of silica and lignin limits the utilization of these wastes as potential feedstock for biological treatment. Therefore, this study investigated the impact of alkali (NaOH) pre-treatment at varied concentration of 2%, 4%, 6%, 8%, and 10% (w/v)) on lignin and silica removal at 90 °C so that the silica can be recovered as a value-added product and the lignin free biomass can be utilized as feedstock to estimate the biogas generation at mesophilic temperature (35 ± 2 °C) for 45 days. The impact of pre-treatment was studied and supported by the SEM, FTIR for morphological, and compositional variations while the AD is supported by 16 s rRNA metagenomic sequencing. Results revealed that increasing the concentration of NaOH up to 8% improved silica extraction with a purity of 97.34% with simultaneous lignin removal by 50 – 70%. Pretreatment with 2% NaOH was more effective in facilitating the accessibility of cellulose and hemicellulose to microbes during AD. In summary, this study concludes 2% NaOH treatment is ideal for both silica and biogas recovery.