Rustic Roots & Modern Finds

Protein-Packed Vanilla Mini Muffins

Made with Fresh-Milled Flour and Sourdough Discard

Baking with kids is one of our favorite ways to slow down, learn something new, and create food we actually feel good about serving. These protein-packed vanilla mini muffins are a staple in our kitchen—they’re lightly sweet, soft, and made entirely from scratch using fresh-milled flour.

This recipe is especially fun because it starts right at the beginning: milling the grain. From there, we mix the dry ingredients, add the wet ingredients, and bake. It’s a simple, repeatable process that kids can genuinely help with.

Equipment

Need to Have

Grain mill for milling flour (optional)
Mixing bowl
Kitchen scale or measuring cups/spoons
Whisk or spoon
Mini muffin pan
Mini muffin liners or grease for the pan
Oven

Nice to Have

Stand mixer or hand mixer (not required)
Cooling rack
Cookie scoop (for evenly sized mini muffins)

Ingredients

These soft, lightly sweet mini muffins are made with fresh-milled flour, buttermilk, honey, and vanilla protein powder. They’re filling, kid-approved, and perfect for breakfast or snacks. Makes approx. 48 mini muffins.

1½ cups fresh-milled soft white wheat flour (≈ 180 g)
⅓ cup vanilla protein powder (≈ 40 g)
(I used Just Ingredients Vanilla Bean, but any vanilla protein powder will work)
1½ teaspoons baking powder (≈ 6 g)
½ teaspoon baking soda (≈ 3 g)
½ teaspoon fine salt (≈ 3 g)
¾ cup buttermilk (6 oz / ≈ 180 g)
½ cup sourdough discard (≈ 120 g)
½ cup honey (≈ 100 g)
2 large eggs (≈ 100 g, without shells)
¼ cup melted butter (≈ 60 g)
½ cup unsweetened applesauce (≈ 120 g)
1 teaspoon vanilla extract (≈ 5 g)

How to Make Protein-Packed Vanilla Mini Muffins

Step 1: Mill the Flour

Mill your wheat berries into fresh flour. Fresh-milled flour behaves a little differently than store-bought flour, but it adds incredible flavor and nutrition. See notes if you’re using store-bought flour.

Step 2: Mix the Dry Ingredients

In a large bowl, whisk together the fresh-milled flour, protein powder, baking powder, baking soda, and salt until evenly combined.

Step 3: Mix the Wet Ingredients

In a separate bowl, mix together the buttermilk, sourdough discard, melted butter, honey, eggs, applesauce, and vanilla extract.

Step 4: Combine

Pour the wet ingredients into the dry ingredients and gently mix until just combined. Do not overmix—the batter should be thick but scoopable.

Step 5: Bake

Preheat your oven to 350°F. Fill mini muffin cups about ¾ full. Bake for 10–12 minutes, or until the tops spring back lightly when touched and a toothpick comes out clean.

Step 6: Cool & Enjoy

Let the muffins cool slightly before removing from the pan. These are perfect warm or once fully cooled.

Recipe Note: Using Store-Bought All-Purpose Flour

If you’re using store-bought all-purpose flour instead of fresh-milled flour, make the following adjustments:

Use 1¼ cups (150 g) all-purpose flour instead of 1½ cups fresh-milled flour
Expect the batter to be slightly thinner
No other ingredient changes are needed

Fresh-milled flour absorbs more liquid than commercial flour, so reducing the flour amount helps keep the muffins soft and prevents them from becoming dense.

Why We Love These Muffins

Made from scratch with real ingredients
Protein-packed and filling
Perfect for little hands
Great for breakfast, snacks, or lunchboxes
Easy to adapt with add-ins later

Storage Tips

Store at room temperature for 1–2 days
Refrigerate for up to 5 days
Freeze in an airtight container for longer storage