This present work studies the potential of different deep eutectic solvents (DES) for green synthesis of nanocellulose. Choline chloride-based DES including choline chloride-oxalic acid (ChCl–OA), choline chloride-urea (ChCl–Ur), choline chloride-imidazole (ChCl–Im), choline chloride-glycerol (ChCl–Gly) and choline chloride-acetic acid (ChCl–AA), and betaine-based DES including betaine-acetic acid (BET-AA) and betaine-glycerol (BET-Gly) were used to synthesis nanocellulose from microcrystalline cellulose (MCC). The physical properties of viscosity, pH, appearance, and functional groups as well as the nanocellulose yield of all synthesized DES were evaluated and compared, accordingly. The results show that the pH of the DES ranges from strong acidic (ChCl–OA) to strong alkaline (ChCl–Ur). The viscosity results show a wide range from the lowest viscosity of ChCl–OA DES (55 cP) to the highest viscosity of BET-Gly DES (1516.67 cP). The appearance of the nanocellulose suspension after the first post-neutralization shows the highest turbidity with ChCl–OA DES, indicating a high presence of nanocellulose. The nanocellulose after drying appears as fine, off-white to slightly translucent powder. The Fourier transform infrared (FTIR) spectroscopy analysis provides the structural analysis of the nanocellulose and shows the presence of all common absorption peaks of cellulose, indicating the chemical structure of cellulose maintained its stability during the hydrolysis process. Furthermore, the choline chloride-based DES showed significant results in the recovery of the nanocellulose as compared to the betaine-based DES. The highest nanocellulose yield of ± 33.6% was presented by the ChCl–OA DES, which was 20.77% higher than that of the lowest BET-AA DES. A strong acidic DES could promote a faster and more effective breakdown of amorphous regions in cellulose. The results provide insights into the potential of DES as a safer and more environmentally friendly method for nanocellulose synthesis.