Chocolate Chip Coffee Muffins – Clean Eating, Gluten Free!

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With a classic, domed top and a gorgeously soft and light inner crumb that’s studded with pockets of warm dark chocolate, these coffee-infused muffins are the perfect gluten-free afternoon pick me up or a great way to kick start your day!

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Coffee Muffins -VS- Coffee Cake

Not to be confused with the more traditional coffee cake which dates back to the 17th C and are simply cakes that are made to be enjoyed with a cup of coffee. (Though, if that is what you’re after, you are in luck because I have a fantastic recipe for just that purpose! Check out my Gluten-Free Blueberry Streusel Muffins!) These muffins are coffee-flavored muffins, infused with the wonderfully rich and aromatic notes of (your favorite) coffee and baked up to be enjoyed as a caffeinated breakfast or mid-afternoon pick me up! Even better, these muffins are studded with dark chocolate to give you a positively mocha-like experience in a conveniently portioned, handheld muffin form! Seriously, what’s not to love? And the best part? Making them is incredibly easy. But first…

Here’s Why You’ll Love These Muffins 🧡🧁

• These muffins are both clean-eating, gluten-free and lacto/ovo vegetarian friendly.
• It’s made using simple, wholesome ingredients.
• They are so easy to make and take just around 35-40 minutes from start to finish!
• They make a great breakfast, afternoon pick-me-up or dessert option.
• Each muffin contains 4g of fiber and 7g of protein!
• Made using coffee, they’re a great caffeinated treat that has amazing depth of flavor. Speaking of which…
• You can make them using your favorite fresh brewed or instant coffee or…
• If coffee isn’t your preference, you can easily omit the use of it to make a great chocolate chip muffin!
• They can be enjoyed fridge-cold, room temp, or warmed.
• They freeze well for later enjoyment.

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Ingredients (and Substitutions)

Here are the ingredients we’ll need for our muffins as well as potential substitutions you can make.

• Almond Flour: Opt to use a super fine-grind of blanched almond flour for the best texture and crumb.
  • Substitution: You can also use almond meal which is almond flour made using almonds with the skin on, the texture of your muffins will be slightly coarser.
• Gluten Free Flour: Using gluten-free flour helps to give our muffins more typical muffin-like bake and texture that you get from regular muffins. Two brands that work great in this recipe is King Arthur’s Measure-for-Measure or Bob’s Red Mill 1-1.
  • Substitution: If you don’t want to use gluten free flour blend, you can replace it with the same amount of almond flour but reduce the liquid/milk by about 2 tbsp. Note that this won’t give you as good a rise/muffin top or texture as you’d get when using the gluten-free flour blend.
• Coconut Sugar: Coconut sugar is one of my favorite sugars to use in my baked goods not only because it’s one of the healthier clean eating sugars but also because of its amazing caramel undertones.
  • Substitution: You can also use equal amounts of finely blended raw cane sugar for this recipe if you prefer
• Dark Chocolate Chips: I am using a combination of 60% and 80% dark chocolate for a bit of taste variety. A great tip is to cut your chocolate into irregular shards and pieces for a more variated bite.
• Olive Oil: I like to use a light olive oil for this recipe.
  • Substitution: You can also use extra light olive oil  or mild olive oil. If preferred, you can also use any other neutral-flavored clean eating oil of your choice or even butter.
• Whole Milk: Using whole milk is a great way to get a soft crumb and moist texture.
  • Substitution: If you want to keep this recipe dairy-free you can use any unsweetened dairy-free milk of your choice such as almond or oat. Just note that certain ones like coconut may alter the flavor slightly.
• Instant Coffee: Opt to use your favorite brand of instant coffee granules. Don’t use ground coffee as they will not dissolve and will make your muffins gritty. However, if you only have ground coffee or…
  • Substitution: …if instant coffee isn’t your preference, no problem! In that case I recommend brewing as much of your favorite coffee as you would for two cups using 1/3 cup of water (basically a strong brew). Use this brew to replace 1/3 cup of milk in the recipe.
• Vanilla: You can use either vanilla bean paste or vanilla extract for this recipe.
• Egg: I’m using whole large US standard eggs.
• Baking Powder: Our main rising agent that will give our muffins the best cake-like texture.
• Salt: I’m using a Himalayan pink salt but you can also use sea salt if preferred.
• Ground Nutmeg: A small touch of this warming spice plays nicely with the coffee and chocolate in this recipe.
  • Substitution: If you like you can swap the nutmeg with a pinch of ground cinnamon powder.

*Quick note: the following pictures for this post were made when I was whipping up a half batch of the recipe (so 6 muffins) but the recipe card itself contains the full 12-muffin recipe.*

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How to Make Your Muffin Batter

Before we start our batter, we’re going to do two things: first we’re going to preheat our oven to 425°F and the second thing we need to do is thoroughly grease our muffin tins with butter or oil (seriously, make sure there’s no ungreased spots and be sure to grease the tops of the tin as well! – or if you prefer you can line them with cupcake liners.

In a large bowl, add your dry ingredients – almond flour, gluten-free flour blend, coconut sugar, baking powder, salt, and nutmeg – and mix them together until fully combined.

To your milk, stir in your instant coffee granules. If it doesn’t fully dissolve that’s okay.

Do I Need To Use Coffee At All?

Honestly, you don’t need to. The coffee in this recipe is purely for flavor. If you’re not a fan of the caffeine content of coffee, I recommend using your favorite decaf so you get the phenomenal coffee flavor, but if you don’t want to include the coffee at all, you can omit it and the recipe will still make a killer chocolate chip muffin!

Now we’ll bring our batter together. To the dry ingredients make a well in the middle and add the milk/coffee mixture, the egg, oil, and vanilla and combine your wet ingredients fully with your dry ones. Then, fold in your chopped dark chocolate to complete your batter.

Note: if you notice that your batter is a bit thick, you can add 1-2 tbsp of additional milk or water to thin it out slightly.

Working quickly, divide your batter evenly into your pre-greased (notice how I’ve butter-greased the tops of the tin too? This guarantees my muffins will pop right out with no effort after being baked!) or lined muffin tins and now it’s time to bake!

Bake Your Muffins – Using this Bakery “Secret” Technique!

Pop your muffins into the oven and let them start baking at 425°F for the first 5 minutes only. Notice in the middle image above how you can see that the edges got some very quick vertical rise? That’s exactly what we’re looking for!

Then, drop the temperature down to 350°F and allow them to bake a further 20-25 min until they are cooked through and a toothpick inserted into the middle comes out clean. See how after baking the tops have risen in the middle and we have our iconic little domed muffin tops? 🤤

Why Do We Start Our Bake Off High and Then Drop The Temperature?

This is sort of a bakery “secret” that helps our muffins to achieve that iconic muffin top. Since the initial heat is so high, it kicks our rising agent into overdrive and causes our muffins to rise upwards quickly. At this point they’re in a fragile and sensitive state so it’s important that you don’t open the door or disturb them, just lower the heat to 350°F. Dropping the heat stabilizes the temperature and allows our muffins to continue to rise and finish baking through.

Once your muffins have finished baking, remove them from the oven and allow them to sit for 5-10 minutes to cool and set up. If you try to remove them too soon they might fall apart from being too warm. Tell me your kitchen doesn’t smell like baked goodness!

Once cooled, you can gently remove your muffins from the tin. If you’ve used a paper liner then you can lift them right out, if you’ve done what I have and used just a greased the tin then a great unmolding method is to place the tips of your fingers around the top edge of the muffin and very gently wiggle it around. If your tins were thoroughly greased, you should feel the edges release easily and the muffin come loose. Or if your muffin tops haven’t spread too far across the top of the tin, you can insert a blunt knife down into each mold and gently run it around the edge to loosen it and pop  your muffins out.

I like to loosen mine and set them askew in the tin to cool even further. Doing this ensures that the steam inside and on the bottom of the tins escape so you don’t get the dreaded soggy bottom…did anyone else read that in Paul Hollywood’s voice? 😂

Let’s Review the Best (Bakery) Tips and Tricks For These Muffins!

• Use a combination of blanched almond flour and a gluten-free flour blend for the best crumb texture.
• Use a combination of dark chocolate percentages for an extra depth of flavor.
• Cut your chocolate into irregular chunks and shards to add a bakery-style irregularity and dispersion, making each bite unique.
• Use milk! It’s going to not only add body and richness to your muffins, but it will also help your muffins brown and bake with an incredibly moist crumb texture.
• Start baking your muffins at a high temperature for the first 5 min and then drop the temperature to encourage that iconic muffin top to form.

These heavenly little caffeinated muffins are great however you enjoy them, fresh baked, room temp, chilled, their rich and deep coffee flavor melds perfectly with the dark chocolate and slight sweetness and caramel notes of the coconut sugar, and I bet you wouldn’t know they were gluten-free unless you were told! Did you try this recipe? What did you think of it? Let us know in the comments below!