Previous studies have shown that light quality and quantity affect methane emissions from plants. However, the role of photoperiod in plant-derived methane has not been addressed. We studied the effects of two photoperiods—long-day (16 h light/8 h dark), and short-day (8 h light/16 h dark)—on growth and methane emissions of lettuce (a long-day plant), mung bean (a short-day plant), and tomato (a day-neutral plant) under a temperature regime of 22/18 °C. All species were grown under both light durations. First, seeds were germinated in Petri dishes for one week, then plants were transferred to pots and randomly assigned to one of the two experimental conditions. Under each condition, twelve plants were grown for 21 days; at that time, plant growth and physiological traits, including plant dry mass, growth index, photosynthesis, chlorophyll fluorescence, total chlorophyll, nitrogen balance index, flavonoids, and anthocyanin, were measured. Lettuce plants under the short-day photoperiod had the highest methane emissions. Long-day plants that were exposed to short-day conditions and short-day plants that were exposed to long-day conditions were stressed; day-neutral plants were also stressed under short days (p< 0.05). All three species had decreased total dry mass under short-day conditions, most likely because of decreased photosynthesis and increased transpiration and stomatal conductance. Methane emission was positively correlated with shoot/root mass ratio, nonphotochemical quenching and anthocyanin; but was negatively correlated with stem height, dry mass, photosynthesis, water-use efficiency, total chlorophyll, and flavonoids (p < 0.05). This study revealed that, besides light intensity and quality, light duration can also affect methane emissions from plants.