Rutabaga is a cool-season root vegetable suitable for long term storage. The tubers were stored for more than 17 weeks. During this time, quality parameters, such as dry weight content, firmness, colour as well as individual sugars, organic acids, glucosinolates and phenolics were evaluated. We studied the chemical composition of rutabaga and investigated the changes during. The content of total sugars from 452 g kg−1 DW increased immediately after harvest up to 726 g kg−1 DW and then slightly decreased to 562 g kg−1 DW; similar trends were observed in the content of glucose, fructose and glucose. The content of organic acids mainly decreased during storage. An increase in phenolic content was observed in the rutabaga tubers during the first three months of storage in a cold store but this later decreased. The content of glucosinolates changed during long term storage but after four months again achieved values comparable with those at harvest time. The 4-month storage still provides a rich content of primary metabolites and bioactive compounds, as the content of phenols increased by more than 60% and sugars by 24%, despite a decrease in glucosinolates by 13% and organic acids by 25–54% compared to values at harvest.