Recipe: Gluten-Free Chocolate Cupcakes

Dessert Recipes

By: Chris Freytag, CPT

It’s hard not to love a chocolate cupcakes, but most of the time they’re loaded with sugar and if you use a box mix they can be full of preservatives and artificial additives. Not these! We have made our gluten-free cupcakes using organic ingredients, sugar alternatives plus a can of pumpkin to keep these healthy cupcakes moist and delicious without adding unhealthy calories.

Taste-tested by my entire family these cupcakes are a winner and everyone will love them!


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    Healthy Cupcake Ingredients

    When it comes to baking healthy cupcakes it’s all about using trusted, safe ingredients. Trust me when I say, I’ve tried so many alternative ingredients and these are the products that are safe to eat AND still taste like what you expect.

    • Navitas Organics Cacao Powder: Organic, Non-GMO, Fair Trade, Gluten-Free
    • Bob’s Red Mill Gluten Free 1-to-1 Baking Flour
    • Otto’s Naturals Cassava Flour: Gluten-Free and Grain-Free Flour For Baking, Certified Paleo & Non-GMO Verified, Made From 100% Yuca Root
    • Organic pumpkin puree: Pumpkin is extremely high in antioxidants and beta-carotene, which can help regenerate cells in the body making pumpkin a tasty and effective “anti-aging” food.
    • Avocado Oil has a mild flavor and is a great alternative to vegetable oils that can be very inflammatory.
    • Maple Syrup is our sugar alternative in this healthy cupcake recipe. Please read
      the ingredients on your maple syrup– there should only be ONE: pure maple syrup. If there are any others listed, throw it in the garbage!
    • I use an egg in this recipe. You can actually skip it if you are egg-free. the pumpkin does a sufficient job holding these cupcakes together.
    • The milk and vinegar create homemade buttermilk. I like making my own so that I can use goat milk. I haven’t experienced using nut milks but if you do, let me know how it turns out!
    • You’re making gluten-free cupcakes so you have to be sure your baking powder is also gluten-free. When I started doing gluten-free baking I didn’t realize there was a difference so it’s worth mentioning!

    Tips For Making This Gluten-Free Cupcakes Recipe Yes You Can enjoy a moist and delicious cupcake with this simple, healthy chocolate cupcake recipe that everyone will love!

    Spoon your gluten-free flour into the measuring cup or use a scale to measure.

    Mik the dry ingredients separate from the wet and when combining make sure you don’t over-mix.

    Don’t overfill your muffin cups

    Gluten-Free Cupcake Frosting Options

    Greek Yogurt Frosting (sugar-free recipe)

    Simple Mills Organic Chocolate Frosting (Premade, Gluten-Free, Vegan, Made with Organic Coconut Oil)

    Quick Buttercream Frosting:

    Use 6 oz of butter (or vegan butter) and 5 ounces of 70% (or higher) dark chocolate, roughly chopped.

    Melt butter and dark chocolate together in a small saucepan until smooth, stirring constantly.

    Pour into a bowl and refrigerate for 20-30 minutes. Once cooled, remove chocolate and whip with a handheld mixer for 2-3 minutes until fluffy. Lather buttercream over cooled cupcakes.

    Gluten-Free Vairations

    Sprinkles are fun topping decoration but watch out for the generic ones in the grocery store, they are filled with harmful dyes and ingredients. I love Supernatural Sprinkles They are natural, nonpareils, contain no artificial dyes, are soy-free, gluten-free, and vegan.

    Depending on the occasion, you may want to get creative with coloring your batter. Supernatural Food Coloring is my go-to food dye powder. It comes in 4 Natural Colors, No Artificial Dyes, Gluten-Free, and Vegan.

    This healthy cupcake is also a perfect option for a baby’s first birthday. It’s highly recommended to refrain from introducing a baby to added sugar until later in life but who can say no to giving a one-year-old a cake to smash?

    I’ve made this same cupcake recipe in small spring form pans for my son’s first birthday and it turned out wonderful!

    babys first birthday cake with fun decorations


    • 1 cup pumpkin puree
    • 1/4 cup avocado oil
    • 1/4 cup maple syrup
    • 1 egg lightly beaten
    • 1 teaspoon vanilla extract
    • 1 cup 1 to 1 gluten-free flour
    • 1/2 cup cassava flour
    • 1 teaspoon baking powder
    • 1/2 teaspoon baking soda
    •  cocoa powder
    • 1/4 teaspoon salt
    • 1/2 cup milk (I use goats milk)
    • 1/2 tablespoon white vinegar

    Total Time: 35 minutes

    Yield: 24 serving(s)


    • 1 box Immaculate chocolate cake mix
    • 1 (16-ounce) can pumpkin
    • 2 large egg whites
    • 1/2 cup water
    • Optional Buttercream
    • 6 tablespoons butter
    • 5 ounces 70% (or higher) dark chocolate, roughly chopped
    • OR
    • Coconut butter


    1. Preheat oven to 350 degrees. Line cupcake pans with 24 cupcake liners.
    2. In an electric mixer, beat chocolate cake mix, pumpkin, egg whites, and 1/2 cup water for 2 minutes to create a smooth batter.
    3. Pour batter into the prepared cupcake liners, filling them about 2/3 of the way full.
    4. Bake 20-24 minutes, or until a toothpick inserted into the center of a cupcake comes out mostly clean.
    5. While the cupcakes are baking, melt butter and dark chocolate together in a small saucepan until smooth, stirring constantly. Pour into a bowl and refrigerate 20-30 minutes.
    6. Once cooled, remove chocolate and whip with a hand held mixer for 2-3 minutes until fluffy. Lather buttercream over cooled cupcakes.
    7. Alternatively, for a lower calorie/lower fat frosting, scoop a few tablespoons of coconut butter from the center of the jar. Warm in the microwave for a few seconds and drizzle over cupcakes.

    Nutrition Information Per Serving

    Serving Size: 1 cupcake

    Calories: 175

    Protein: 4 gram(s)

    Fat: 6 gram(s)

    Carbohydrates: 25 gram(s)

    Fiber: 2 gram(s)

    Sugar: 14 gram(s)

    Recipe Cuisine: American

    From the kitchen of:

    Rate this Recipe

    1 Star2 Stars3 Stars4 Stars5 Stars (27 votes, average: 4.04 out of 5)


    on Reply

    Where do you buy Immaculate mix? I have checked Lunds/Byerlys, Kowalskis, Cub, Target and Valley Natural Foods. The link to Amazon is a different brand name. Thanks!

      on Reply

      Hi Cindy! Huh - I used to be able to get it at most grocery stores but you're right, it looks like it might be harder to find now. Although, I think I did see it available on Instacart. Another brand you could use is Annie's if you're looking for a more natural cake mix brand.

    on Reply

    If you can't find immaculate mix, can you use ANY boxed mix?

      on Reply

      Hi Debi, yes you can use whatever box mix you like. We just like Immaculate mixes as they are free from artificial flavors, preservatives and hydrogenated oils!

    on Reply

    What about just cake mix & pumpkin? I do that with a spice cake mix. Just cake mix & pumpkin...yum!## And no more added sugar

      on Reply

      Do you still bake at box temp. for the time given for cupcakes?

      on Reply

      That would work! We have two ingredient muffins that are similar!

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