The colour of honey is one of the most important quality criteria for consumers. The colour depends mainly on the content of plant pigments but the honey consistency, shape, and size of the crystals may also influence the honey colour parameters. It is related to the crystallisation and decrystallisation processes of honey during storage. In the present study, directions of colour changes of honey during storage were evaluated using a tristimulus colorimeter and the CIE 1976 L*a*b* and CIE L*C*ho systems. The effect of time (3 and 9 months) and storage conditions (cold storage, room temperature storage with access to light, and room temperature storage without access to light) on the colour of nectar honeys was investigated. The results obtained showed that both the type of honey and the storage conditions influenced the honey colour parameters. Significant differences in direction and intensity of the colour changes of honey during storage were observed. These differences make it difficult to indicate which storage conditions are optimal to preserve the colour of the honey. It was found that acacia and heather honeys were the most susceptible to colour changes during long-term storage in all of the study’s applied conditions, whereas rape and buckwheat honeys were the most stable in colour parameters.