
Chocolate Almond Flour Muffins
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These almond flour muffins are a delicious breakfast or snack that tastes like a treat. They’re dotted with dark chocolate pieces, and we add collagen. They’re naturally gluten- and dairy-free and ready in just 30 minutes!

On busy mornings, I rely on easy grab-and-go breakfasts like these chocolate almond flour muffins. They’re rich and chocolatey — honestly, more like brownies than muffins — and perfect for meal prep or a quick bite alongside a cup of coffee.
They’re just as good warmed up, too. Sometimes I’ll serve one with a scoop of ice cream and call it dessert, which feels like a pretty great bonus for something that started as breakfast.
Ingredients notes
- Coconut sugar: coconut sugar is less processed than regular sugar. You can use cane sugar or brown sugar if that’s what you have on hand. You’ll see we don’t use very much because almond flour has a natural sweetness to it.
- Coconut oil: melted (and cooled) coconut oil is what we use but avocado oil also works.
- Almond flour: for this recipe, use a fine-ground almond flour rather than almond meal which tends to be more coarse.
- Collagen: We use unflavored collagen in these muffins. Our go-to collagen brand is Vital Proteins, but you can use a different brand of collagen – just test it with hot water first to make sure it doesn’t gel.
- Pecans: we use pecans for a nutty crunch, but chopped walnuts make a great alternative. You can also omit the nuts altogether if you prefer.
Other ingredients you need are eggs, vanilla extract, cocoa powder, baking powder, sea salt, hot water, and chopped dark chocolate. Oh, and some flaky sea salt for sprinkling on top (if desired).

What to serve with almond flour muffins
These almond flour muffins are delicious on their own as a breakfast or snack. We usually have two with a creamy almond butter latte! Serve them as part of a brunch spread, or pack them for a picnic. We always keep some in the freezer to warm one up and top with a scoop of coconut milk ice cream when we need a sweet fix!
Recipe FAQs
Can I freeze these muffins?
Absolutely, these muffins freeze really well. Store them in a reusable bag or an airtight container in your freezer for up to three months.
What’s the best type of chocolate chunk to use?
We use a dark chocolate bar and roughly chop it into pieces. You can also use store-bought chocolate chunks or chocolate chips. We like the Enjoy Life brand.
Can I omit the collagen?
Yep! Omitting it won’t affect the recipe at all.
Can I use coconut flour instead of almond flour?
No, coconut flour isn’t a great substitute for almond flour. It is much drier and more absorbent than almond flour, so you’d have to make more changes to the recipe overall.
Watch to see how to make these muffins

Almond Flour Muffins Recipe
Ingredients
- ⅓ cup coconut sugar
- ⅓ cup melted coconut oil
- 4 large eggs
- 1 tablespoon vanilla
- 2 cups almond flour
- ¾ cup cocoa powder
- ¼ cup 4 scoops collagen (see notes)
- 2 teaspoons baking powder
- ½ teaspoon sea salt
- ½ cup hot tap water
- ½ cup chopped dark chocolate (or paleo chocolate chips)
- ½ cup chopped pecans
- Optional: flaky sea salt to top the muffins
Instructions
- Preheat your oven to 350 degrees Fahrenheit. Line a 12-cup muffin tin with liners.
- Add the coconut sugar, coconut oil, eggs, and vanilla to a large bowl and beat with electric beaters.⅓ cup coconut sugar, ⅓ cup melted coconut oil, 4 large eggs, 1 tablespoon vanilla
- Add the almond flour, cocoa powder, collagen, baking powder, and sea salt and beat until just combined. Add the hot water and carefully beat it into the batter. Fold in the chocolate and pecans.2 cups almond flour, ¾ cup cocoa powder, ¼ cup 4 scoops collagen, 2 teaspoons baking powder, ½ teaspoon sea salt, ½ cup hot tap water, ½ cup chopped dark chocolate, ½ cup chopped pecans
- Divide the batter between the lined muffin cups, filling them nearly to the top. For extra chocolaty muffins, top with a few chocolate chips or chunks.
- Bake the muffins for 12-20 minutes – see the guidelines below. Let the muffins cool for 5 minutes before removing them from the muffin tin. Optional: top with a little sprinkle of flaky sea salt.Optional: flaky sea salt to top the muffins
Notes
Nutrition
We have thoroughly tested this recipe for accuracy. However, individual results may vary. See our full recipe disclosure here.


Hi Kristen. Can I use protein powder instead of collagen? Is it 13 grams of protein PER muffin?
Hi Julie. I haven’t tried it with protein powder so I can’t say for sure, but I suspect it would be ok. This recipe is pretty forgiving.