How to Make Healthy Muffins From Scratch

How to Make Healthy Muffins From Scratch

Before we get started, let me tell you how much I LOVE muffins. Easy to whip up. Easy to make in large batches. Easy to freeze for busy mornings. I even like to serve them for dinner if we’re having a soup or stew. Sound weird? You might be thinking of the “might-as-well-be-a-cupcake” types of muffins that we see everywhere these days. That, my friends, is not a true muffin.

If you’re looking for a sweet, dessert-style muffin, you won’t like this recipe, so no hard feelings from me if you move on. But if you’re looking for something delicious that you feel good about eating and serving your kids in the morning….look no further. This is it. Absolutely no artificial ingredients or weird chemicals that are found in the boxed muffin mixes, and YOU have control over the amount of sugar in the recipe.

Here’s my basic recipe, and also some of my favorite ways to switch it up.


  • 1/4 cup plain yogurt (or sub 1/4 cup oil, butter, or applesauce)
  • 1 medium egg
  • 1 cup milk
  • 1/4 cup sugar (omit for a savory muffin)
  • 1/4 teaspoon salt
  • 1 tablespoon baking powder
  • 1 cup unbleached, all-purpose flour
  • 1 cup flour of your choice (cornmeal, whole wheat flour, rye, or more all-purpose flour)
  • Optional: Vanilla


Preheat oven to 400 degrees. Line a muffin tin with paper liners or grease muffin cups well with oil. If you have silicone muffin cups, those work great and don’t require any extra greasing.

In a glass bowl, stir together the yogurt, egg, milk, sugar and salt. (If using vanilla, add in now)

Whisk together until a bit frothy with a fork. Add in the baking powder and flour(s). Stir together until all of the flour is moistened but be careful NOT TO OVER MIX. Aim for 30 strokes of your fork or less.

Spoon batter into prepared muffin cups. (Tip: I like to use a 1/4 cup to evenly measure into 12 cups.)

Bake at 400° for 18 – 20 minutes. Remove from the oven and cool slightly before removing from the pan.


My family’s favorite combo is cornmeal and vanilla. These are so good with some butter and jam and a steaming cup of coffee.

If you use Rye flour, skip the vanilla and sugar and add in some caraway seeds. This version is great with soup.

When I use oat flour, I like to sub in brown sugar and some raisons.

Whole wheat flour is good with an addition of fresh or frozen berries.

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