The right amount of leavening is key
We were already making rich chocolate brownie-style muffins from a batter that's made ahead, refrigerated, and then scooped and baked daily, so I knew the concept was feasible. But when I first tried refrigerating my other muffin batters (including cornmeal-cherry muffins and pumpkin-spice muffins), I wasn't successful. After a few days in the fridge, the batter would become too liquid to scoop, and the muffins would come out flat and heavy. Why didn't these batters work as wonderfully as the chocolate muffins? I realized that the biggest problem was the chemical leaveners -- the baking powder and baking soda -- in the other batters. (The chocolate muffin has no chemical leaveners.) So I focused my experiments on the leaveners.
Leaveners give muffins lift and keep them tender. Eliminating the leaveners for these muffins was never an option. The leaveners in muffins and other baked goods make them light and tender and give them lift. (Because the chocolate muffin is denser--more brownie-like than muffin-like -- it works well using eggs alone as the leavener.) Getting the correct ratio of leavening seemed to be the trick to creating a batter that would store well.
Chemical leaveners work by reacting with acids to create carbon dioxide, the same gas that yeast produces. Baking soda begins to create gas when moistened. Double-acting baking powder (which most baking powders are these days) produces an initial set of gas bubbles when mixed with wet ingredients and then a second set when heated. The first reaction forms many small gas cells in the batter; the second reaction expands the bubbles to create a light texture.
The problem with trying to store a batter that contains baking soda or baking powder is that the leavening agents continue to produce gas bubbles until they're used up. Over time, those bubbles will collapse, resulting in dense muffins with little loft.
Adding more leavening helps -- as long as it isn't too much. What seemed to work best was to add a little baking soda to recipes that had only called for baking powder, but I had to be careful not to add too much. A funny thing happens with chemical leaveners. Food scientist Shirley Corriher describes it this way: with too much leavening, the gas bubbles get too big, they run into each other, float to the top of the batter, and escape.
Once I added baking soda, I had to consider that it can leave a soapy taste behind. So in each recipe, I neutralized that soapy quality with acidic ingredients such as sour cream, buttermilk, yogurt, or lemon juice. The added acid seemed to improve the batter's shelf life. I also cut back on the liquid ingredients so that the chilled batter wouldn't liquefy over time.