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The pretreatment of lignocellulosic biomass such as <i>Miscanthus</i> grown on marginal agricultural land is very challenging and requires severe conditions to fractionate cell wall polymers for further valorization. The current study aimed to determine organic acid-based mild conditions to pretreat contrasting lignocellulosic <i>Miscanthus</i> genotypes for the efficient fractionation of cell wall components, with special focus on hemicellulose extraction. In doing so, five <i>Miscanthus</i> genotypes were subjected to four different acid treatments (sulfuric acid, oxalic acid, malonic acid, and citric acid) in a vertical high-pressure steam sterilizer. The results demonstrated that, among the organic acids, oxalic acid was identified as the most effective pretreatment solvent for hemicellulose separation, whereas citric acid yielded the highest amount of galacturonic acid, varying from 15 to 17 mg mL⁻¹ across genotypes. One best performing genotype was selected for the enzymatic hydrolysis. Overall, <i>M. floridulus</i> genotypes exhibited the optimal quality traits for efficient bioconversion with second best in terms of ethanol production potential.