Damage resulting from harvest operations increase the storage losses of sugar beet. Because of different equipment, the kind and extent of damage may differ between harvesting systems. The objective of the study was to analyze (I) the impact of different harvesting systems and cleaning intensities on damage of sugar beet, and furthermore, (II) the effect of these damages on storage losses. In 2015 and 2016 at 4 sites, two sugar beet varieties were harvested with two six-row harvesters using three cleaning intensities with three replicates in tracks of 200 m length. Roots were stored in a climate container at 9 °C. The results show that the diameter of root tip breakage and surface damage increased markedly with cleaning intensity. Considerable differences occurred among varieties and sites. The factor analysis indicates that the extent of damage (root tip breakage, surface damage) had a considerable impact on the infestation with mould and rots, the accumulation of invert sugar and sugar losses after storage. The marked impact of the cleaning intensity emphasizes the importance of the driver and of the optimal adjustment of the harvester for a good harvesting quality and thereby storability of beet.