Agricultural byproducts rich in lignocellulose are considered one of the most promising feedstocks to produce sustainable value-added materials with different industrial applications. However, fractionation into carbohydrates, lignin, and silica is a key challenge in the conversion of plant biomass into value-added products due to its complex structure. This study is designed to develop a novel method for sequential separation and collection of cellulose, hemicellulose, lignin, and silica from agricultural byproducts, peanut shell (PS), rice husk (RH), and sugar cane bagasse (SB), using an integrated approach under mild hydrolysis conditions. Silica and cellulose nanofibers (CNFs) were synthesized using an ultrasonic-assisted chemical method. Pure silica was obtained by further pyrolysis. The yield percent of cellulose was 35\%, 39\%, and 41\% and hemicellulose and lignin combined was 30\%, 18\%, and 29\% from PS, RH, and SB, respectively. The X-ray diffraction results demonstrated that CNFs were semicrystalline from all samples, and CNFs from SB had the highest crystallinity. Similarly, silica nanoparticles (SNPs) were amorphous in RH, while it was crystalline in both PS and SB. The surface morphologies of the CNFs and nanosized fibers were observed by field emission-scanning electron microscopy. It revealed that there were different morphological characteristics such as web-like, parallel, and tangled in PS, RH, and SB, respectively. The surface morphology of SNPs was also varied among the samples. In BET analysis, SNPs from RH had a larger specific surface area of 37.5 m(2)/g and total pore volume of 0.08 cc/g compared to SNPs from both PS and SB. The ascribed method could be a potential approach for comprehensive utilization of agricultural biomass through a relatively simple process, which can then be used for the biorefinery process or as a feedstock for the biomaterials industry. It is also suggested that the structural variations of CNFs/SNPs might be a vital factor to be considered for selecting optimal biomaterials.