Chocolate Beet Muffins Made with Fresh Milled Flour

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If I told you these muffins had beets in them AND if I told you my kids DEVOUR them every time I make them, you might question my sanity. Welcome to wonderful (delicious chocolate beet muffins that is)!

baked chocolate beet muffins on a cooling rack

This is the kind of recipe I make when I want something homemade that feels like a treat but still uses real, nourishing ingredients. They are perfect for breakfast, snacks, or on-the-go eating.

Love beets like me and want more recipes using them? Try making Beet Pizza Crust, Beet Hummus, Beet Pasta Sauce, or Beet Brownies.

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Why You’ll Love These Chocolate Beet Muffins

These chocolate beet muffins are soft and fluffy with just the right amount of flavor. The roasted beets quietly do their job, adding moisture and natural sweetness while letting the chocolate take center stage. Pair that with fresh milled flour, and you’ve got a muffin that’s both comforting and nutritious.

Super Food: the perfect recipe to use up all those garden goodies and get your antioxidants; the beets add nutrition without changing the flavor. Plus these are naturally sweetened with maple syrup!
Beautiful: Who doesn’t love mixing up a pink batter? They end up more of a deep purple color instead of a bright pink once baked.
Whole Grain Goodness: Fresh milled flour adds a warm, nutty depth you can actually taste, but it isn’t overwhelming. It’s like a healthy version of a chocolate cupcake!
Simple: No mixer needed! Just a bowl and a spatula will get the job done.

Chocolate Beet Muffin Recipe

Tools

Grain Mill
Danish Whisk
Mixing Bowl
Muffin tin + paper liners (or grease it well)
Spatula
Measuring cup and spoons
Kitchen Scale
Cooling Ra c k

Ingredients

2 Eggs
120 grams Beets, roasted, peeled, and blended
56 grams Unsalted Butter, melted
150 grams Maple Syrup
2 teaspoons Vanilla Extract
135 grams Greek Yogurt
190 grams Soft White Wheat
25 grams Cocoa Powder
1/2 teaspoon Baking Soda
1 teaspoon Baking Powder
1/2 teaspoon Salt
50 grams Mini Chocolate Chips (optional, but highly recommended)

Notes

You can substitute sour cream for Greek yogurt if that’s what you have on hand
Can use coconut oil or avocado oil in place of butter
I will switch between using soft white wheat and spelt (or a combination of the two) when I make these
Makes 12 muffins

Step-By-Step Fresh Milled Chocolate Beet Muffins

Prep: If you haven’t yet roasted your beets, do that first. I usually roast a bunch of beets at a time, then freeze them for later use. If you already have your beets roasted, go ahead and preheat your oven to 375°F and prepare a muffin tin with liners and/or grease.

Roasting Beets

Roast: Preheat oven to 400°F. Wash and wrap fresh beets in foil, and roast for 45–60 minutes, or until fork-tender.
Blend: Add roasted beets to a blender with a splash of water if needed and blend until smooth.
Peel: Let cool, then remove peels. Wear gloves if you don’t want pink hands.
Add to Recipe: Use in recipe as needed or freeze in an ice cube tray for easy portions.

Mix Batter: In a large bowl, whisk together all of your wet ingredients.

process shots of mixing up a pink muffin batter using roasted beets, cocoa powder, flour, and eggs

Fold in dry ingredients, just until combined.

dark pink muffin batter in a glass bowl with a blue spatula

Add-Ins: Fold in chocolate chips. We prefer using the mini chocolate chips.

chocolate beet muffin batter with chocolate chips on top in a glass bowl with a blue spatula

Portion and Rest: Divide the batter evenly among the muffin cups, then let it rest on the counter for 10 minutes to ensure the flour is hydrated.

pink muffin batter in the liners in the baking pan

Bake: Bake for 16–20 minutes, until a toothpick inserted in the center comes out clean or the internal temperature is 200 degrees.

baked chocolate beet muffins still in the muffin pan

Cool: Let cool slightly in the pan for a couple of minutes before removing. Cool fully before serving…or don’t. Warm chocolate muffins are hard to resist. You don’t even need butter on these!

muffins on a cooling rack on top of a kitchen towel

Chocolate Beet Muffin Variations

Dairy-Free: Use neutral oils instead of butter and dairy-free chocolate chips.
Extra Chocolate: Sprinkle chocolate chips on top before baking for more chocolatey goodness or try adding a teaspoon of instant coffee to enhance the flavor.
Mini Muffins: Bake for 12–14 minutes for snack-size treats.
Nutty: Add in chopped pecans or walnuts for a little crunch.

These chocolate beet muffins are one of those recipes that feel a little sneaky, but totally decadent. Cozy, rich, and nourishing, and perfect for sharing with people you love (even if you don’t tell them there are beets inside).