These double chocolate flaxseed mini muffins are the perfect healthy snack for toddlers and pack well in school lunches for kids.

Filled with chocolatey goodness, these muffins are a healthy dose of fiber and omega-3 fatty acids thanks to the ground flaxseeds in the recipe.

So do you and the ones you love a favor and make these tasty little chocolate muffins. You’ll be glad that you did!

Jump to Recipe – Print Recipe

Why you’ll love these double chocolate flaxseed mini muffins

Bursting with chocolate flavor: Although these may be good for you, they definitely don’t taste like your typical health food. As if chocolate batter wasn’t enough, these flaxseed muffins are also filled with mini chocolate chips.

Provides healthy amount of fiber: Fiber is an essential element of good digestion and helps regulate blood sugar. Flaxseeds and whole wheat flour together make these muffins fiber powerhouses.

Easy for little mouths to enjoy: Normal sized muffins can prove challenging to eat for toddlers and little kids. Mini muffins are much easier to enjoyfor those little people in you life. Heck, grownups will also appreciate the small size, making it easy to pop one in and enjoy.

Easy to make: With a simple ingredients list and uncomplicated batter method, these muffins are super easy to make. When the fancy strikes, you can have these mini treats made in no time!

Ingredients and substitution ideas

At the bottom of the post you’ll find the detailed recipe with the exact measurements. Here I’ll give you a brief overview of what’s in these mini muffins:

Ground flaxseeds – Flaxseed meal is used in lieu of eggs in this mini muffin recipe. I like the nutrition they provide as well their great binding ability.
Whole wheat flour – The foundation of the batter. Whole wheat flour is a good source of nutrients, but you can use all-purpose flour if you prefer.
Cocoa powder – The first of the two types of chocolate used in this recipe. Cocoa powder makes the batter deliciously chocolatey.
Baking powder and baking soda – Together these ingredients provide great lift to the muffins, helping avoid a dense crumb that is sometimes the norm for whole grain baked goods.
Salt – An essential to help enhance the flavor of any baked good.
Coconut oil – Makes the muffins perfectly moist without being too oily. You can use any neutral oil you like.
Almond milk – Use almond milk or you favorite alternative milk if avoiding dairy. If you’re not avoiding dairy, you can use cow’s milk as well.
Coconut sugar – I found the perfect amount to add to the recipe to make these muffins just the right amount of sweet without being overly so. The recipe calls for coconut sugar, but regular granulated sugar works well too.
Apple cider vinegar – The addition of apple cider vinegar helps the muffins rise. It also helps the muffins be extra tender.
Vanilla – This extract complements the chocolate beautifully and makes the mini muffins so good.
Mini chocolate chips – Mini chocolate chips incorporate best amongst the mini muffins, but regular chocolate chips work too.

How to make chocolate mini muffins

Making these double chocolate mini flaxseed muffins couldn’t be easier. Here’s the basic steps:

Heat the oven to 350 degrees Fahrenheit and grease or line a 24-cup mini muffin tin with cupcake liners.
Hydrate the ground up flaxseeds for 5 minutes.
Mix together the flour, cocoa powder, baking powder, baking soda, and salt. Set aside.
Whisk the melted coconut oil, room temp almond milk, coconut sugar, apple cider vinegar, and vanilla in with the hydrated flaxseed meal.
Combine the dry ingredients and the wet ingredients until no streaks of dry flour remain.
Add in the mini chocolate chips and stir until they’re evenly distributed throughout the batter.
Bake for 15 minutes in the hot oven. Remove the muffins from the oven and let cool for 10 minutes.
Enjoy warm or at room temperature.

See, it’s as simple as that!

Tips for making mini muffins

Following these tips will help you make the very best double chocolate mini muffins.

Melt the coconut oil and warm up the almond milk together. Coconut oil is usually solid at room temperature (depending on the temperate of your kitchen) and needs to be melted to evenly incorporate into the batter. To melt the oil, as well as warm up the milk, put them together in a microwave safe bowl and microwave in 30 second bursts until the coconut oil is melted.
Use mini chocolate chips. Mini chocolate chips will more evenly disperse throughout the batter, making sure each mini muffin has gooey, gooey chocolate morsels. If you only have normal sized chocolate chips, you can chop them up smaller using a serrated knife before adding them to the batter.
Sift the cocoa powder. Cocoa powder tends to clump up while being stored. Sift it through a fine mesh strainer into the flour to get rid of all the lumps. This will make sure there are no unpleasant blobs of unsweetened cocoa powder in your muffins.
Evenly divide the batter among the muffin tin with a spring loaded scoop. Getting batter evenly distributed among regular muffin tins can be tricky, let alone a mini muffin tin. Make it easier by using a spring loaded cookie or ice cream scoop that holds about 1 TBS of batter. That’s the perfect amount for each mini muffin cup.
Use the amount of sugar called for in the recipe. I’m one who tries to get away with as little sugar in a recipe as possible, but I have tried this recipe with less sugar and was disappointed. 50 grams of sugar made muffins that were flavorful and moist. Less sugar made dry, flavorless, sad muffins.

Storing extra muffins

These flaxseed muffins make great snacks and are also a fantastic addition to a school lunch. Here’s how to store them to ensure they stay moist and tasty.

Store the muffins in an airtight container on the counter. They’ll stay fresh for 3 – 4 days this way.

Freeze the muffins for longer term storage. Simply place them in an air-tight freezer safe container or freezer bag for up to 3 months of storage time.

When you want to eat one (or a few), take as many as you want out of the freezer and let them defrost on the counter for a few hours. For quicker thawing, pop them in the microwave for 30 seconds or so. Let cool slightly then enjoy.

Double Chocolate Flaxseed Mini Muffins

May 1, 2024

These double chocolate flaxseed mini muffins are the perfect healthy snack for toddlers and pack well in school lunches for kids. Filled with chocolatey goodness, these muffins are a healthy dose of fiber and omega-3 fatty acids thanks to the ground flaxseeds in the recipe.

Print Pin

Prep Time 10

Cook Time 15

Total Time 25

Course Breakfast

Cuisine American

Servings 24 mini muffins

Ingredients

¼ cup whole flaxseeds (40 g) or ½ cup flaxseed meal
½ cup water
1 ¼ cups whole wheat flour (175 g)
3 TBS cocoa powder (25 g)
2 tsp baking powder
½ tsp baking soda
½ tsp salt
⅓ cup coconut oil (70 g) melted
½ cup almond milk (100 g) room temp
¼ cup coconut sugar (50 g)
1 TBS apple cider vinegar
2 tsp vanilla
½ cup mini chocolate chips

Instructions

Put an oven rack in the middle position of the oven. Heat the oven to 350℉. Grease or line with paper baking cups a 24-cup mini muffin tin.
Grind the flaxseeds until fine in a small food processor, blender, or spice grinder. Combine the ground flaxseeds and water in a large bowl. Let sit 5 minutes.
¼ cup whole flaxseeds, ½ cup water
In a medium bowl, whisk together the flour, cocoa powder, baking powder, baking soda, and salt.
1 ¼ cups whole wheat flour, 3 TBS cocoa powder, 2 tsp baking powder, ½ tsp baking soda, ½ tsp salt
In the large bowl with the soaked flaxseeds in it, add the melted coconut oil, room temp almond milk, sugar, apple cider vinegar, and vanilla. Whisk to combine.
⅓ cup coconut oil, ½ cup almond milk, ¼ cup coconut sugar, 1 TBS apple cider vinegar, 2 tsp vanilla
Pour the flour mixture in with the flaxseed mixture. Mix until combined.
Add the chocolate chips and mix until evenly distributed.
½ cup mini chocolate chips
Divide the batter among the cups of the mini muffin tin. Put in the heated oven and bake for 15 minutes.
Let cool 10 minutes. Enjoy!