Gluten-Free Baked Chocolate Donut Holes

These gluten-free baked chocolate donut holes are soft, chocolatey, and ready in 30 minutes. Perfect for busy mornings and easy enough for beginners!

Last Saturday morning, my daughter peeked into the kitchen and asked if we could make donuts together. I’ll be honest—my first thought was “not today!” because traditional donuts feel like an all-day project. But then I remembered these gluten-free baked chocolate donut holes, and suddenly the answer was yes.

Here’s what I love about this recipe: it comes together in one bowl, bakes in about 10 minutes, and tastes like those chocolate cake donuts you’d find at your favorite bakery. No deep frying, no fancy equipment, just a mini muffin pan and ingredients you probably already have.

These gluten-free baked chocolate donut holes have become our Sunday morning tradition. They’re tender, perfectly sweet, and covered in a simple vanilla glaze that makes them irresistible. Whether you’re new to gluten-free baking or you’ve been at it for years, this recipe is forgiving and fun.

The best part? According to the Celiac Disease Foundation, maintaining a strict gluten-free diet is essential for those with celiac disease, but that doesn’t mean you have to give up your favorite treats.

These baked gluten-free donut recipes prove that delicious comfort food is absolutely possible without gluten.

Gluten-Free Baked Chocolate Donut Holes Ingredients

Chocolate Donut Holes

• 1/4 cup butter, melted
• 1/2 cup maple syrup (room temperature)
• 1/2 cup plain Greek yogurt (I prefer Fage 2%)
• 1/2 cup milk of choice (skim, 2%, whole or almond), heated to room temperature
• 2 tsp vanilla
• 2 eggs
• 2 cups gluten-free all purpose flour
• 1 tsp baking soda
• 1/2 tsp salt
• 1/2 cup cocoa powder

Glaze

• 2 cups powdered sugar
• 8-10 tsp milk
• 1 tsp vanilla extract (optional)

Instructions

Chocolate Donut Holes

1. To begin, preheat your oven to 350°F. Spray a mini muffin pan with non-stick spray in each muffin cavity.
2. To a large mixing bowl, add your butter and maple syrup and whisk them together. Add your Greek yogurt, milk and vanilla and whisk till combined. Add your eggs and briefly mix them in.
3. To the same bowl, add your flour, baking soda and salt. Add a fine mesh strainer over the bowl, and sift your cocoa powder into the bowl. Stir till you have a thick, smooth donut batter.
4. Using a small cookie scoop, scoop the donut batter into each mini muffin cavity till they’re all filled.
5. Bake in the oven for 9-11 minutes, or till spongy to touch and a toothpick inserted comes out clean. Let them cool partially, then flip them out onto a cooling rack.

Glaze

1. To a mixing bowl, add your powdered sugar and 8 teaspoons of milk (and vanilla). Whisk till smooth. If your glaze is too thick, add one more teaspoon of milk.
2. Dip each donut hole into the glaze and roll it around till covered entirely. Gently shake any excess glaze off into the bowl, then place back on the cooling rack (with a pan underneath for glaze drips). Repeat till all of the donut holes have been glazed.
3. Devour!

Substitutions & Swaps

One of my favorite things about these gluten-free baked chocolate donut holes is how adaptable they are. Let me walk you through some swaps that work beautifully.

Dairy-Free Options: If you need these completely dairy-free, swap the butter for coconut oil (melted and cooled slightly) and use your favorite plant-based yogurt. Coconut yogurt works wonderfully here. For the milk, almond milk or oat milk are both perfect choices.

Sweetener Swaps: Not a fan of maple syrup? Honey works just as well, though it’ll give a slightly different flavor profile. You could also use agave nectar in a pinch.

Flour Flexibility: I’ve tested these baked gluten-free donut recipes with several flour blends. Bob’s Red Mill 1-to-1 and King Arthur Measure for Measure both work beautifully. Just make sure your blend contains xanthan gum—it helps give these little treats their tender texture.

Greek Yogurt Alternatives: Regular yogurt or even sour cream can step in for the Greek yogurt. You might need to reduce the milk slightly if using regular yogurt since it’s thinner.

Chocolate Intensity: Want even more chocolate flavor? Toss in 1/2 cup of mini chocolate chips to the batter. My kids request this version constantly, and honestly, I’m not mad about it.

These gluten-free donut holes baked in a mini muffin pan are forgiving, so don’t stress if you need to make a swap or two. They’ll still turn out delicious.

Troubleshooting Tips

Let’s talk about the little hiccups that might happen—and how to fix them quickly.

Dry or Crumbly Donut Holes: This usually means your batter was a bit thick or they baked a touch too long. Make sure your milk and maple syrup are at room temperature before mixing—cold ingredients can make the batter seize up. Also, check them at 9 minutes. Gluten-free baked goods can go from perfect to overdone quickly.

Dense Texture: If your gluten-free baked chocolate donut holes turn out heavy, your baking soda might be past its prime. Give it a freshness test: drop a little into vinegar. If it doesn’t fizz vigorously, grab a new box.

Donut Holes Sticking: Even with non-stick spray, sometimes these little guys want to stick. Let them cool for about 5 minutes in the pan before trying to remove them. A small offset spatula can help gently coax them out.

Glaze Too Runny: Start with 8 teaspoons of milk and add more gradually. Different brands of powdered sugar absorb liquid differently. You want a glaze that’s pourable but not watery—it should coat the back of a spoon.

Cocoa Powder Lumps: This is why I always sift! Those little lumps refuse to break down once mixed in. Take the extra 30 seconds to sift your cocoa powder through a fine mesh strainer.

Most issues with healthy gluten-free chocolate chip muffins or donut recipes come down to timing and temperature. Trust your instincts—if they spring back when touched, they’re done.

Storage & Meal Prep

Here’s the deal with storing these gluten-free baked chocolate donut holes: they’re best enjoyed fresh, but life happens and sometimes you need to plan ahead.

Room Temperature Storage: These will stay fresh in an airtight container at room temperature for about 2 days. After that, they start to lose their soft texture. Pop a piece of bread in the container with them—it helps keep them moist.

Refrigerator Storage: If you need them to last longer, store them in the fridge for up to 5 days. Let them come to room temperature before serving, or warm them for 10-15 seconds in the microwave.

Freezing Instructions: These freeze beautifully! Place unglazed donut holes in a single layer on a baking sheet and freeze until solid. Transfer to a freezer bag and store for up to 3 months. When you’re ready, thaw at room temperature and glaze them fresh.

Make-Ahead Tips: You can mix the dry ingredients the night before and store them in a bowl covered with plastic wrap. In the morning, just whisk together the wet ingredients and combine. Your baked gluten-free donut recipes will come together even faster.

Glaze Prep: The glaze is best made fresh since it sets quickly. It literally takes 2 minutes to whisk together, so I don’t usually prep it ahead.

Pro tip: these gluten-free donut holes baked fresh on a Sunday morning make the whole house smell amazing. But honestly, I’ve been known to pull a few from the freezer on a random Wednesday afternoon when we need a pick-me-up.

Serving Suggestions & Pairings

Let’s talk about the fun part—how to serve these little chocolate treasures. While they’re absolutely perfect on their own, here are some ideas that’ll make them even more special.

Weekend Brunch Spread: Arrange your gluten-free baked chocolate donut holes on a pretty platter alongside fresh berries and a bowl of whipped cream for dipping. Add some coffee and you’ve got yourself a cozy brunch situation.

After-School Snack: My kids love these with a cold glass of milk or a warm cup of hot chocolate. It feels indulgent but they’re actually a bit healthier than store-bought donuts thanks to the Greek yogurt and lack of deep frying.

Party Treats: These are fantastic for birthday parties or school celebrations. They’re the perfect two-bite size, and you can make them even more festive with colored glazes or sprinkles.

Pairing Ideas: These baked gluten-free donut recipes pair beautifully with fresh fruit—especially strawberries or raspberries. The tartness balances the sweetness perfectly. They’re also wonderful with a hot latte or cappuccino for a café-style experience at home.

Holiday Twist: During fall, I sometimes add a pinch of cinnamon to the batter. For the holidays, peppermint extract in the glaze instead of vanilla creates a chocolate-mint situation that everyone loves.

If you’re looking for more gluten-free breakfast ideas, try my creamy dairy-free oat milk pumpkin pie or vegan pumpkin pie for a complete morning spread.

These gluten-free baked chocolate donut holes are versatile enough for any occasion. They’ve saved me more than once when unexpected guests drop by.

Variations & Dietary Adjustments

Want to mix things up? These gluten-free baked chocolate donut holes are incredibly adaptable for different tastes and dietary needs.

Vanilla Version: Skip the cocoa powder and increase the flour by 1/2 cup. You’ll have vanilla donut holes that are just as delicious. Add 1/2 teaspoon of almond extract for extra flavor.

Kid-Friendly Tweaks: If your little ones aren’t huge chocolate fans (does that even exist?), reduce the cocoa to 1/4 cup for a lighter chocolate flavor. You can also press a few mini chocolate chips into the top of each one before baking.

Dairy-Free Adaptation: As mentioned earlier, use coconut oil, plant-based yogurt, and non-dairy milk. The texture stays beautifully tender. These healthy gluten-free chocolate chip muffins principles work perfectly here too.

Lower Sugar Option: Cut the maple syrup to 1/3 cup and add 1/4 cup of unsweetened applesauce. For the glaze, try using a powdered sugar alternative designed for baking. The donut holes won’t be quite as sweet, but they’re still totally enjoyable.

Protein Boost: Swap half of the Greek yogurt for protein powder mixed with a bit of extra milk. Chocolate protein powder works especially well in this recipe.

Cinnamon Sugar Coating: Skip the glaze entirely and roll the warm donut holes in a cinnamon-sugar mixture. This creates more of a churro-style treat that’s absolutely addictive.

Filled Donut Holes: Use a piping bag to fill the center of each donut hole with Nutella, jam, or pastry cream after baking. It takes them to a whole new level of decadence.

These baked gluten-free donut recipes are a blank canvas for your creativity. Don’t be afraid to experiment and make them your own.

Gluten-Free Baked Chocolate Donut Holes FAQs

Why These Gluten-Free Baked Chocolate Donut Holes Work

There’s actual science behind why this recipe is so reliable, and I think it’s worth understanding if you’re diving into gluten-free baking.

The Greek yogurt and melted butter work together to create moisture and richness that gluten-free baked goods often lack. The yogurt also adds a subtle tang that balances the sweetness beautifully.

Baking these as mini muffins instead of full-size donuts is genius for gluten-free baking. The smaller size means they cook quickly and evenly, which prevents that sometimes-gummy texture that can happen with gluten-free treats.

According to research on gluten-free baking techniques, using a flour blend with xanthan gum helps create structure and prevents crumbling. That’s why choosing the right flour matters so much.

The combination of baking soda with the acidity from the yogurt creates a beautiful rise and tender crumb. It’s why these gluten-free baked chocolate donut holes come out so soft and cake-like rather than dense or heavy.

Sifting the cocoa powder isn’t just fussy baker behavior—it actually prevents those annoying lumps and ensures even chocolate distribution. Trust me, I’ve skipped this step before and regretted it.

Final Thoughts

These gluten-free baked chocolate donut holes have earned a permanent spot in our family’s recipe rotation. They’re the kind of recipe that makes gluten-free baking feel easy and approachable, which is exactly what we all need.

Whether you’re making them for a special breakfast, packing them in lunchboxes, or just treating yourself on a random Tuesday, they bring a little joy to the day. And isn’t that what good food should do?

If you try these baked gluten-free donut recipes, I’d love to hear how they turn out for you. Feel free to get creative with the variations, and don’t stress about making them perfect. Some of my best batches have been the “oops, I forgot to add that” experiments.

For more comforting gluten-free recipes that the whole family will love, check out my dairy-free chicken pot pie recipe with curry option. It’s another one-bowl wonder that makes weeknight dinners feel special.

Happy baking, friend! May your kitchen always smell like chocolate and your donut holes always be perfectly glazed