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Background Lignin in sugarcane bagasse (SB) hinders its utilization by microorganism, therefore, pretreatment methods are employed to make fermentable components accessible to the microbes. Multivariate analysis of different chemical pretreatment methods can aid to select the most appropriate strategy to valorize a particular biomass. Results Amongst methods tested, the pretreatment by using sodium hydroxide in combination with methyltrioctylammonium chloride, an ionic liquid, (NaOH+IL) was the most significant for xylanase production by Bacillus aestuarii UE25. Investigation of optimal levels of five significant variables by adopting Box-Behnken design (BBD) predicted 20 IU mL− 1 of xylanase and experimentally, a titer of 17.77 IU mL− 1 was obtained which indicated the validity of the model. The production kinetics showed that volumetric productivity of xylanase was much higher after 24 h (833.33 IU L− 1 h− 1) than after 48 h (567.08 IU L− 1 h− 1). The extracted xylan from SB induced more xylanase in the fermentation medium than pretreated SB or commercially purified xylan. Nuclear Magnetic Resonance, Fourier transform infrared spectroscopy and scanning electron microscopy of SB indicated removal of lignin and changes in the structure of SB after NaOH+IL pretreatment and fermentation. Conclusion Combined pretreatment of SB with alkali and methyltrioctylammonium chloride appeared better than other chemical methods for bacterial xylanase production and for the extraction of xylan form SB.