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Almond Flour Protein Muffins on a plate

Chocolate Almond Flour Muffins

Kristen Stevens
By: Kristen Stevens
Updated: 04/15/2025
4.9 stars (37 ratings)
36 Comments
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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!

Almond Flour Protein Muffins on a plate

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).

Almond Flour Muffins in a baking pan

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.

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4.92 stars (37 ratings)
Almond Flour Protein Muffins on a plate

Almond Flour Muffins Recipe

Prep: 10 minutes mins
Cook: 20 minutes mins
Total: 30 minutes mins
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These almond flour muffins are a delicious breakfast or snack that tastes like a treat. They're dotted with chunks of dark chocolate, and we sneak in some collagen.. They're naturally gluten- and dairy-free and ready in just 30 minutes!
12

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

Fudgy dessert muffins: 12-14 minutes. Soft and delicate muffins that hold their shape: 16-17 minutes. Firm muffins that hold their shape: 18-20 minutes.
To prevent the muffin liner from sticking, make sure to let the muffins cool completely before taking it off.
This recipe was tested using Vital Proteins Collagen Peptides. If you use a different brand, test if first to make sure that it doesn’t gel when added to hot water. 

Nutrition

Serving: 1 muffin, Calories: 313kcal (16%), Carbohydrates: 17g (6%), Protein: 13g (26%), Fat: 25g (38%), Saturated Fat: 10g (63%), Polyunsaturated Fat: 2g, Monounsaturated Fat: 4g, Trans Fat: 1g, Cholesterol: 62mg (21%), Sodium: 216mg (9%), Potassium: 125mg (4%), Fiber: 5g (21%), Sugar: 7g (8%), Vitamin A: 93IU (2%), Vitamin C: 1mg (1%), Calcium: 98mg (10%), Iron: 2mg (11%)
© Author Kristen Stevens

We have thoroughly tested this recipe for accuracy. However, individual results may vary. See our full recipe disclosure here.

Almond Flour Protein Muffins on a plate

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Almond Flour Protein Muffins on a dessert plate with ice cream

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Kristen Stevens

Kristen Stevens

Hi, I'm Kristen! I LOVE everything to do with food: making it, taking pictures of it, and (the best part) eating it. ♡♡♡

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Posted: 08/24/2018 Updated: 04/15/2025
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36 Comments
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Julie
Julie

Hi Kristen. Can I use protein powder instead of collagen? Is it 13 grams of protein PER muffin?

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Kristen Stevens
Kristen Stevens
Reply to  Julie

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.

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Welcome!

Hi, I'm Kristen Stevens

I’m a self-taught chef, food photographer, and author of the cookbook Sugar Free Dinner Recipes. Since 2011, I have been sharing my well-tested and approachable recipes, helping home cooks like you feel comfortable and confident in the kitchen. My work has been featured in Food & Wine, Pioneer Woman, The Every Girl, Self, and many more. Let’s have some fun cooking together!

Learn more!

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