From Steve Magness:
"A common yet surprising result of including two runs in a day is that you often feel more recovered the following day. The most obvious reason is that by running shorter twice, you don’t beat your body up as much as you would on a longer single run. On these shorter runs you have plenty of fuel stores and rely primarily on your heavily fatigue-resistant slow-twitch muscle fibres. The result: no lingering fatigue or damage. Instead, you get an increase in blood flow twice to help with recovery and, perhaps more importantly, an increase in hormones (such as growth hormone) that help with recovery. Getting a good hormonal spike to aid recovery twice during a day does wonders for getting you recovered for the next day’s workout.
But the benefits of doubles go beyond just recovery. One workout by itself doesn’t translate to a sudden increase in fitness. Instead, each run triggers the body to signal certain genes to make functional adaptations. It takes multiple runs or workouts to translate that signal into some sort of functional change. Essentially, you need an accumulation of stimuli to get the training adaptations you work so hard for.
Doubling plays a role in this in two ways. A general aerobic training stimulus twice per day instead of once means that the genes that cause desirable changes, such as increased mitochondria (the structures within cells that produce energy) or an increase in oxygen-carrying capacity, are activated for a greater total time than if you did just one run. So you have a much more sustained pressure on adaptation.
Also, by running doubles, especially after a hard workout, you’re training in a pre-fatigued state. Doing so allows you to access different muscle fibres that you might not normally train, or to push further into the depths of glycogen depletion than you would normally. As a result, you get a slightly different stimulus for adaptation. Research looking into training twice a day versus once a day for the same total weekly volume has shown that the increases in aerobic enzymes (proteins that facilitate energy production) can be potentially greater when doing two bouts of exercise relatively close together."