Healthy Chocolate Muffins with Greek Yogurt (Gluten Free)

These healthy chocolate muffins with chocolate chips are a sweet treat to have on hand for a snack on-the-go, breakfast or even dessert! With lower sugar than most chocolate muffins, they're moist, delicious, and easy to make with nutritious and simple ingredients like eggs, Greek yogurt and applesauce. Gluten-free too!

Got a hankerin' for a double chocolate muffin that's gluten-free, delicious and simple to make?

Ok, that's a pretty specific hankering but if you are in that camp, I've got you covered!

This recipe for healthy chocolate muffins is perfect for when you want something sweet (but not too sweet) and want to keep it on the healthier side of the fence.

If you love gluten-free muffins of all sorts, check out these Healthy Cranberry Oatmeal Muffins, this recipe for Healthy Gluten Free Apple Muffins with Cinnamon or these Gluten-Free Blueberry Muffins with Coconut Flour.

Jump to:

• 🥣Ingredients
• 📝Instructions
• 🔄Substitutions
• 💃Variations
• 🔪Equipment
• 🥡Storage and Freezing
• ✅What makes these healthy chocolate muffins healthier than most other chocolate muffins?
• 📖 Recipe

🥣Ingredients

Everything you'll need to make these healthy chocolate muffins is probably already in your cupboard, pantry and fridge.

Here's what you need:

• Gluten-free flour - I like Bob's Red Mill 1:1 Baking flour. This one has xanthan gum in it. Xanthan gum is a natural binding agent used in gluten-free baking. You need it when baking with gluten-free flours because it's the gluten in wheat flour that acts as the binding agent. If you use a gluten-free flour that doesn't have xanthan gum (or make your own gluten-free flour blend) you have to addd xanthan gum so that the muffins will have a spongy well, muffin-like texture!
• Cocoa powder - look for "Dutch process", as most are and really any brand will do the job, just be sure it doesn't have any added sugars or sweeteners
• Baking soda
• Baking powder
• Salt
• Applesauce - unsweetened
• Milk
• Greek yogurt - 2%, non-flavoured
• Eggs
• Vanilla - optional
• Chocolate chips - I prefer Hersey's Dark (gluten free)

See? Simple ingredients, right?

See recipe card for quantities and details.

📝Instructions

Making these muffins is supa-dupa easy.

High-level steps are:

1. Add the dry ingredients in a medium or large bowl and combining with a whisk
2. Combine the wet ingredients in another medium bowl and whisking up until combined
3. Pour the wet ingredients into the large bowl with the dry and stir until combined
4. Add the chocolate chips last and give the muffin batter a final stir
5. Divide the batter among the muffin pan and bake in a pre-heated oven for ~20 minutes or until an inserted toothpick comes out clean and the tops of the muffins are springy

🔄Substitutions

• Egg substitute - if you're looking to make these muffins egg-free, you can use an egg substitute like a "flax egg" to get a similar effect as actual eggs. To make a flax egg, mix 3 tablespoon of water with 1 tablespoon of ground flax seed for each egg. In these muffins, you'd need to make 2 of these flax eggs (one for each egg.)

• Dairy-free - to make these muffins dairy-free, I would recommend using a dairy-free milk (oat or almond for example) but to also add 2 tablespoon of white vinegar to the milk to almost create a buttermilk substitute. This won't be perfect but will add some of the "tang" that the Greek yogurt brings.

• No applesauce? No problem! Substitute the applesauce for over-ripe mashed bananas. You can use those browning bananas on the countertop for these muffins. You'll get the natural sweetness like the applesauce brings and a little more fibre (bonus!)

💃Variations

Some fun add-ins for these gluten-free muffins would be:

• Cherries - chocolate and cherry is one of those universally amazing flavour combinations. Yum city🏙️ Why not add a few diced bing cherries when you're stirring in the chocolate chips?
• Raspberries - likewise with the point above: raspberries and chocolate gluten-free muffins are right up flavour alley

Looking for a use for that coconut flour in your cupboard? Do NOT sub coconut flour 1 for 1 in this (or any) recipe. Why? Because coconut flour acts like a sponge! It really soaks up any fluid in your batter. To incorporate coconut flour, try replacing ⅓ cup of the 1:1 gluten-free baking flour with coconut flour. And just be aware: it's a totally different flour to work with😅

If you want to try a gluten-free blueberry coconut muffin, give these Gluten-Free Blueberry Muffins with Coconut Flour a try!

🔪Equipment

You just need some pretty typical equipment for these muffins: muffin tins (12-cup), silicone baking cups (or the paper ones will work too), a medium mixing bowl and a larger mixing bowl, a whisk, a large spoon or spatula and a cooling rack for the muffins.

🥡Storage and Freezing

Since these gluten-free muffins are so moist and packed with wet ingredients, keep them stored on the countertop in an airtight container with a lid.

These muffins freeze beautifully. Wrap them and store in an air-tight container with a lid. Freeze for up to 3 months. Take them out and let them thaw at room temperature before eating or throw one in your lunch bag in the morning and it'll be thawed by lunchtime!

✅What makes these healthy chocolate muffins healthier than most other chocolate muffins?

• Greek Yogurt - packed with protein, calcium and phosphorus, the Greek yogurt in these muffins not only brings texture and moistness to the crumb, it delivers a punch of nutrition along the way
• Applesauce (or banana) - who doesn't love a little hit of vitamin C, potassium and magnesium from their gluten-free muffin?!
• Low in sugar - with less sugar than most other typical muffins out there, these easy chocolate muffins bring more nutrition for less total sugar and calories

Alright I hope you capital L-love these chocolate muffins like we do!

~April

📖 Recipe