One of the new xylitol producer microorganisms is Barnettozyma populi Y-12728 and it has great potential for the industry with its pure xylitol production capability. Different immobilization strategies, the usability of baffled or normal flasks with different agitation speeds, and various lignocellulosic hydrolysates were studied in this research. The highest xylitol production and yield values were 11.99 g xylitol/L and 40.28 % for the C1 trial at 70 ml medium with a suspended cell. For the immobilization strategy, 1 % polyethyleneimine concentration, 1.5 mm surface lattice thicknesses, and 8 3D cubes were determined to be the optimum conditions with 17.84 g/L xylitol production and 0.473 g xylitol/g xylose yield values in a 70 ml volume medium at 200 rpm, 30 °C, and 6.0 initial pH for 3 days. Rice husk, wheat bran, and oat husk hydrolysates were also used as a substrate for xylitol fermentation. The highest xylitol production was 2.26 g/L for lignocellulosic hydrolysates. In this research, FDM (Fused Deposition Modelling) based 3D printed cubes are used for the immobilization agent of Barnettozyma populi NRRL Y-12728 for the first time. The results revealed that FDM-based 3D-printed cubes could be used to immobilize cells and improve productivity for xylitol production.