Chocolate Chip Flaxseed Muffins
Calling all healthy muffin lovers! These chocolate chip flaxseed muffins are loaded with tastiness without being overloaded with processed ingredients.

Thanks to flaxseeds and whole wheat flour, these muffins are packed with healthy fiber. And when you add mini chocolate chips to the mix, these muffins are transformed from ordinary to extraordinary.
And to top it all off, these chocolate chip loaded muffins are easy to make and are vegan.
Why you’ll love these chocolate chip flaxseed muffins
These chocolate chip flaxseed muffins will quickly become a favorite at your house.
Here’s why you’ll be making this recipe on repeat:
Perfect texture – With a perfectly tender interior, these easy muffins have such a perfect texture.
Healthy ingredients – You don’t need to use white flour and loads of granulated sugar to make a delicious muffin. This recipe embraces wholesome ingredients like flaxseeds, whole wheat flour, and a small amount of coconut sugar to make muffins that both taste good and make you feel good.
Easy to make – When a recipe is this easy to make and so delicious, it’s hard not to make it again and again.

Flax seed muffin ingredients
Not only are these muffins easy to make, but they need a simple list of ingredients that you probably already have on hand.
- Flaxseeds – Ground flaxseeds add fiber, omega-3s, and help bind the batter together.
- Whole wheat flour – A hearty, nutritious flour that gives the muffins a wholesome texture while adding extra fiber.
- Coconut sugar – A natural sweetener that provides a hint of caramel-like flavor without being over processed.
- Coconut oil – Keeps the muffins soft and moist.
- Baking powder and baking soda – These leavening agents work together to help the muffins rise nice and fluffy.
- Vanilla extract – Enhances the sweetness and brings warmth to the overall flavor.
- Almond milk – You could also use dairy milk.
- Apple cider vinegar – Reacts with the baking soda to create lift and fluffiness in the muffins.
- Chocolate chips – The star ingredient! Melty, sweet bites of chocolate make these muffins extra delicious.

How to make chocolate chip flaxseed muffins
Ready to eat one of these tasty muffins? Head to your kitchen, follow these easy steps, and you’ll be happy snacking in no time.
- Prep. Heat your oven to 350 degrees F. Grease or place paper liners into the cups of a 12-cup muffin tin.
- Make a flax egg. Combine the flaxseeds with water and milk. Set aside to thicken.
- Whisk up dry ingredients. Whisk flour, baking powder, baking soda, and salt together.
- Combine wet ingredients. Add coconut sugar, coconut oil, vanilla, and apple cider vinegar to the flax mixture. Whisk to combine.
- Add dry ingredients to wet ingredients. Pour the dry ingredients in with the wet ingredients. Mix until just combined.
- Fold in chocolate chips. Pour in the chocolate chips and gently fold in until evenly distributed.
- Bake. Evenly divide the batter among the cups in the muffin tin. Bake for 25 minutes.
- Cool and dig in. Remove from the oven and let cool for 10 minutes in the pan. Take out of the pan and enjoy warm or let cool entirely on a wire rack.

Tips for successful muffin baking
For the best muffin outcome, take a look at these tips and apply them:
Use room temperature ingredients. Because this muffin recipe calls for melted coconut oil, you really need to make sure the milk you add is not cold. Cold milk will make the coconut oil solidify into chunks. We need the oil to stay melted so it mixes evenly throughout the batter. The muffins will be nice and moist this way.
Don’t over mix your batter. Over mixing will cause the flour to build gluten. This will make the muffins rubbery instead of tender. Only mix until the flour is just combined with the wet ingredients.
Conquer the divide. The best way to evenly divide the muffin batter among the cups of your muffin tin is with a spring loaded cookie or ice cream scoop.
Smooth the tops of the batter before baking. This muffin batter is kind of thick, so smooth the tops of the muffins flat with a rubber spatula or spoon before baking. This will give the muffins a more uniform look as they bake. Although it’s not necessary, it is a nice touch.

Conclusion
These chocolate chip flaxseed muffins are the perfect balance of healthy and delicious!
Made with nutrient-packed flaxseeds, naturally sweetened, and loaded with melty chocolate chips, they make a great breakfast, snack, or treat any time of day.
Plus, they’re easy to make and freezer-friendly, so you can always have a batch on hand.

Chocolate Chip Flaxseed Muffins
April 17, 2024Ingredients
- ½ cup ground flaxseeds (50 g)
- ½ cup water room temp or warm
- ½ cup almond milk (120 g) OR milk of choice, room temp
- 1 ½ cups whole wheat flour (180 g)
- 2 tsp baking powder
- ½ tsp baking soda
- ½ tsp kosher salt
- ⅓ cup melted coconut oil (70 g)
- ¼ cup coconut sugar (50 g) OR granulated sugar
- 1 TBS apple cider vinegar
- 2 tsp vanilla
- 1 cup chocolate chips
Instructions
- Place an oven rack in the middle position of the oven. Heat the oven to 350℉. Grease or line a 12-cup muffin tin.
- Put the ground flaxseeds into a large bowl. Pour the water and milk over the flaxseeds and mix together. Set aside and let sit for 5 minutes.½ cup ground flaxseeds, ½ cup water, ½ cup almond milk
- In a medium bowl, whisk together the flour, baking powder, baking soda, and salt. Set aside.1 ½ cups whole wheat flour, 2 tsp baking powder, ½ tsp baking soda, ½ tsp kosher salt
- To the flaxseed mixture, add the coconut oil, coconut sugar, apple cider vinegar, and vanilla. Whisk together well.⅓ cup melted coconut oil, ¼ cup coconut sugar, 1 TBS apple cider vinegar, 2 tsp vanilla
- Pour the dry ingredients in with the wet ingredients. Using a rubber spatula, gently mix together until no dry flour remains.
- Fold in the chocolate chips until evenly distributed throughout the batter.1 cup chocolate chips
- Evenly divide the batter among the muffin tin. Bake for 22 – 25 minutes.
- Let cool in the pan for 10 minutes, then remove the muffins from the pan and finish cooling on a wire rack. Enjoy warm or at room temperature.