The quality of milled surface medium-density fibreboards (MDF) and the effect of the wrong milling direction during the process of automatic milling in real conditions in practice (production machine, production tool, and material) are presented in the paper. Moreover, the effect of the double vs. single bladed milling cutter on the final surface quality with the simultaneous changes in individual parameters of feed rate, thickness of the removed layer, and cutting direction was investigated. The MDF was separated using the strategy “one per pass“ with required cutting direction (climb or conventional) and the required thick strips cutting off (4 mm to 16+ mm) at a constant operation speed of the milling cutter (n = 20000 min−1) and a changing feed rate from vf = 1 m/min−1 to vf = 5 m/min−1. The use of a multi-bladed milling cutter resulted in the higher quality of the milled surface in all cases (change in feed rate, thickness of removed layer, and cutting direction). The effect of the wrong milling direction during automatic milling was observed only for a single-bladed milling cutter used. An increase in surface roughness (Ra) occurred; therefore, using the double-bladed milling cutter, which was not associated with an increase in surface roughness, is recommended.