Cellulose nanocrystals (CNC) have received great research attention since the last few decades due to their extraordinary properties and wide range of applications. In this study, a sustainable and cost-effective method for the synthesis of lignin-containing cellulose nanocrystals (LCNC) from oil palm empty fruit bunch (EFB) is presented. This method is able to retain the lignin in EFB and manifest the properties of lignin. The proposed synthesis process is simpler than the conventional method of producing lignin-coated CNC by first removing the lignin to synthesize CNC followed by the re-coating of lignin on the structure. The samples of LCNC were characterized by transmission electron microscopy, X-ray diffraction, Fourier-transform infrared spectroscopy and water contact angle analysis. In addition, by altering the acid concentration during acid hydrolysis process (53% - 60% H2SO4), both surface hydrophobicity (66.0° - 75.1°) and length of LCNC (467 nm-177 nm) can be altered wherein a higher concentration of acid resulted in a greater contact angle and a shorter length of LCNC. Cost and energy analysis deduced that the proposed synthesis method saved about 62% of the total material cost and 80% less energy as compared to the synthesis of lignin-coated CNC.