Recipes for muffins, in their yeast-free "American" form, are common in 19th century American cookbooks. Recipes for yeast-based muffins, which were sometimes called "common muffins" or "wheat muffins" in 19th century American cookbooks, can be found in much older cookbooks.

A somewhat odd combination of circumstances in the 1970s and 1980s led to significant changes in what had been a rather simple, if not prosaic, food. The decline in home-baking, the health food movement, the rise of the specialty food shop, and the gourmet coffee trend all contributed to the creation of a new standard of muffin.

Preservatives in muffin mixes led to the expectation that muffins did not have to go stale within hours of baking, but the resulting muffins were not a taste improvement over homemade.

On the other hand, the baked muffin, even if from a mix, seemed almost healthy compared to the fat-laden alternatives of doughnuts and Danish pastry. "Healthy" muffin recipes using whole grains and such "natural" things as yogurt and various vegetables evolved rapidly. But for "healthy" muffins to have any shelf-life without artificial preservatives, the sugar and fat content needed to be increased, to the point where the "muffins" are almost indistinguishable from cupcakes. The rising market for gourmet snacks to accompany gourmet coffees resulted in fancier concoctions in greater bulk than the original, modestly sized corn muffin.

The marketing trend toward larger portion sizes also resulted in new muffin pan types for home-baking, not only for increased size. Since the area ratio of muffin top to muffin bottom changed considerably when the traditional small round exploded into a giant mushroom, consumers became more aware of the difference between the soft texture of tops, allowed to rise unfettered, and rougher, tougher bottoms restricted by the pans. There was a brief foray into pans that could produce "all-top" muffins, i.e., extremely shallow, large-diameter cups. The TV sitcom Seinfeld made reference to this in the "The Muffin Tops" episode in which the character Elaine Benes co-owns a bakery named "Top o' the Muffin to You!" that sold only the muffin tops. Along with the increasing size of muffins is a contrary trend of extremely small muffins. It is now very common to see muffin pans or premade muffins that are only one or two inches in diameter.