overhead shot of healthy chocolate muffins on a baking rack

These healthy chocolate muffins are perfectly moist, and packed with good-for-you ingredients (including carrots!). Kids love these healthy muffins, and you will too!

We know firsthand how much of a struggle it can be to consistently feed your family good, wholesome foods – especially when you have kids who are picky eaters.

That’s why we decided to create an easy recipe that includes good-for-you ingredients, but in a super kid-friendly form: the much-loved muffin!

These double chocolate muffins are naturally sweetened, packed with healthy fats and protein, and even include a hearty serving of vegetables for a nutrition boost. And they’re so fluffy, moist and delicious that your kids will keep coming back for more.

You’ll find yourself serving these veggie muffins all day long: as part of a healthy, quick breakfast with a side of Greek yogurt, as a snack-y lunch with fresh fruit, and heck, you can even add a dollop of whipped cream to make them a better-for-you dessert (they almost taste like chocolate cake!).

And of course, they’re perfect to grab as easy snacks and to pack in your kids’ lunchboxes.

Follow the recipe below to make these healthy chocolate chip muffins – they’re a great choice for your entire family!

PIN for when you want a healthy muffin recipe:

What You’ll Need

To make these healthy chocolate muffins you’ll need the following ingredients (scroll to the bottom for all the specific measurements on the recipe card):

  • Almond flour
  • Gluten-free flour (this can be substituted for an all-purpose or white whole wheat flour)
  • Cocoa powder or cacao powder
  • Coconut sugar (this can be substituted for maple syrup)
  • Baking soda
  • Ground cinnamon
  • Salt
  • Eggs
  • Coconut Oil
  • Unsweetened vanilla almond milk
  • Vanilla extract
  • Carrots
  • Chocolate chips (we recommend the “Enjoy Life” brand)
How to Make Healthy Chocolate Muffins – Step by Step Instructions

First, combine the dry ingredients (flour, cocoa/cacao powder, sugar, baking soda, cinnamon and salt) in a large mixing bowl and set aside.

If you have a sifter, sift the flour into the bowl – you’ll end up with even lighter, fluffier muffins!

Next, in a medium mixing bowl, combine the wet ingredients (eggs, melted coconut oil, almond milk and vanilla extract).

Add the wet ingredients to the dry ingredients. Stir until the mixture is just moistened.

Fold in the shredded carrot and chocolate chips.

Note: If the dough seems too dry, add a splash more almond milk to the mixture and stir to incorporate.

Add muffin liners to a muffin pan and spray with cooking spray (we recommend pure coconut or avocado oil spray). Scoop out the batter into the muffin liners until they’re 2/3rds full.

Add a sprinkle of extra chocolate chips on top if you want.

Bake at 350F for 20-25 minutes, or until a toothpick comes out clean. Remove from oven and cool on a wire rack.

Easy Recipe Adaptions
  • Swap out the coconut sugar for maple syrup
  • Swap the gluten-free flour for any all-purpose flour or kick up the nutrition even more by using white whole wheat flour
  • Add in a ¼ cup of your favorite add-ins like chia seeds, flax or hemp hearts
  • Leave out the chocolate chips if you want to reduce the sugar, or just sprinkle a few on top
  • Experiment with different veggies: this recipe works equally as well with shredded zucchini, or try a mix of shredded carrot + zucchini.
How to Store Your Healthy Chocolate Muffins

Once your hidden veggie muffins have fully cooled, you can store them in an airtight container (we like to line it with a paper towel) at room temperature for up to 5 days.

We always recommend making a double batch as these muffins freeze really well. Simply place them in a plastic freezer bag (remove as much air as possible) and store for up to 3 months. Defrost at room temperature or in the microwave.

Why You’ll Love These Healthy Chocolate Muffins
  • Nutritious Alternative: These little muffins are much healthier than your traditional muffin which can be loaded with refined sugar. This recipe uses natural sweeteners and packs in a ton of extra nutrition with wholesome ingredients, including healthy fats and protein from the almond flour and almond milk, and of course all of the vitamins and minerals from the “hidden” carrot!
  • Easy to Adapt: Use our suggested adaptations above to customize this healthy hidden veggie muffin recipe so it’s perfect for your family.
  • Freezable: Once cooled, these veggie muffins are perfect to wrap up and pop in the freezer. Then you’ll always have a healthy snack (or meal!) on hand when hunger strikes. You can also grab them in the morning to pack in your child’s lunchbox and they’ll be thawed come lunchtime.
  • Anytime Snack or Meal: When a muffin recipe is made from such good-for-you ingredients, you can adapt it to be part of any eating occasion! We love them as part of a quick, healthy breakfast and they make the perfect, poppable snack.
  • Quick & Easy Recipe: You’ll have an entire batch of these healthy chocolate muffins to enjoy in just 35 minutes, start to finish. And you don’t have to get out your food processor or blender – all you need is 2 bowls.
  • Delicious! The best part is that the final results are insanely yummy. These veggie-filled muffins have a moist, fluffy texture and a rich chocolate flavor that will please even the pickiest eaters. Trust us, they will be gone in a heartbeat!
Close-up of chocolate muffins on baking rack

Healthy Chocolate Muffins with Hidden Veggies

These healthy chocolate muffins are perfectly moist, and packed with good-for-you ingredients (including carrots!). Kids love these healthy muffins, and you will too!
Prep Time 10 minutes
Cook Time 22 minutes
Course Breakfast, Dessert, lunch, Snack
Servings 12


Dry Ingredients

  • 3 cups almond flour
  • 1/4 cup gluten-free flour
  • 1/4 cup cocoa powder or cacao powder
  • 1/2 cup coconut sugar *
  • 1 tsp baking soda
  • 1 tsp ground cinnamon
  • 1/2 tsp salt

Wet Ingredients

  • 3 eggs beaten
  • 1/2 cup coconut oil melted
  • 1/4 cup unsweetened vanilla almond milk
  • 1 tsp vanilla extract

Other Ingredients

  • 1 cup shredded carrots
  • 1/3 cup chocolate chips we like the “Enjoy Life” brand


  • Preheat oven to 350 F.
  • Place 12 muffin liners into a muffin tin and spray with cooking spray.
  • Combine dry ingredients in a large bowl: flour (use a sifter if you have one), cocoa/cacao powder, sugar, baking soda, cinnamon and salt.
  • Mix together wet ingredients in a medium size bowl: eggs, coconut oil, almond milk and vanilla extract.
  • Stir wet mixture into dry ingredients until just moistened.
  • Fold in shredded carrots and chocolate chips.
  • Use an ice cream scoop to portion out 12 muffins.
  • Bake for 20-25 minutes or until a toothpick comes out clean.


  • You can substitute coconut sugar for ½ cup maple syrup – just mix in with the wet ingredients instead
  • If dough seems too dry, add a splash more almond milk to the mixture
Keyword healthy snack, muffin

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Lyndsey Piccolino

Lyndsey Piccolino

Lyndsey is a healthy lifestyle blogger and recipe creator at mommafitlyndsey.com. She covers healthy recipes, meal planning & prep, and healthy lifestyle tips and products. She is a life-longer Pittsburgh native where she lives with her husband and two daughters. You can find Lyndsey at Momma Fit Lyndsey, on Pinterest, and Instagram at @lyndsey.picc and @mommafitlyndsey.

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