There is a strong link between circadian and diurnal cycles and the metabolism of mammals and disrupting these cycles can have a profound effect on metabolic parameters. Investigations into the interplay between energy metabolism and circadian rhythms in mice normally use a 12:12 hour light:dark cycle which mimics a day close to the equinox. However, in many countries that are not close to the equator, seasonal variation in light hours can dramatically change between summer and winter. We hypothesised that altering the light:dark cycle can affect both circadian periodicity of specific tissue clocks as well as processes involved in energy storage and utilisation in mice. Male mice were housed at one of three photoperiods, a summer period (18L:6D), a winter period (6L:18D) and an equinox period (12L:12D) and metabolic testing was performed over the course of 12 weeks. We found that a winter photoperiod caused an increase in the rhythmicity of lipid metabolism (plasma NEFA, RER and lipid oxidation genes) and this was associated with reduced fat mass and liver fat content compared to mice housed on the other photoperiods. The increased rhythmicity disappeared when mice were placed on a time-restricted feeding regime suggesting that the effects on metabolism were due to altering the timing of food intake. Additionally, most rhythmic genes in metabolically important tissues synchronised to the start of the dark phase rather than the start of the light phase suggesting that for these tissues, signals associated with arousal are bigger Zeitgebers than light. Together these results suggest that seasonal light differences can impact mammalian metabolism by altering timing of eating.