Gluten-Free Chocolate Flaxseed Cupcakes


I’m pretty much over the cupcake trend.


Sure, they’re cute and can satisfy a cake craving in one bite. You can make different flavors in one batch. You can experiment with different toppings in the same recipe, or try out your new cupcake tin liners, or enjoy a baked dessert in 20 minutes, or …

Okay. I take it back. I still love cupcakes.


Besides, I’m not going to get rid of my cupcake pans just because cupcakes are so last quinquennium. Cupcakes are perfect for testing out new recipes; mistakes are easily forgiven. Unlike this balancing disaster:



At least these mini-cupcakes are delicious, even if they can’t stay upright for more than the time it takes my camera shutter to fire. As I mentioned in this post, I first tried a variation of this gluten-free cupcake last week and knew I had to make a batch right away. Adding ground flax seed makes these cupcakes both rich in healthy omega-3 fats and perfect for this month’s Recipe Redux theme.

No matter the season, a scattering of seeds can jazz up the flavor, texture and nutrition profile of just about any dish. Whether it’s a chilled chia seed pudding or a hearty roasted vegetable salad with a sunflower seed crunch, show us how you sow your favorite seeds in a recipe reflecting the season in your part of the globe.


How does flax seed represent the season? Well, spring and early summer are a time to clear the home of winter clutter. Part of my spring cleaning routine involves getting rid of extra ingredients, either by giving them away or incorporating them into recipes. It was during this process I found four – FOUR – enormous bags of flax seed in our pantry.

Have I ever mentioned Peter buys in bulk?

And so we have gluten-free chocolate flax seed muffins that are the best gluten-free cupcakes I’ve ever had. The ground flax seed adds a richness that pairs well with chocolate. And they’re a snap to make. Recipe adapted from the fantastic Elana’s Pantry.

Gluten-Free Chocolate Flaxseed Cupcakes

Β  Prep Time: 10 minutes

Β  Cook Time: 10-20 minutes

Β  Keywords: bake gluten-free coconut flour chocolate flaxseed

Ingredients (24 mini or 10 regular)

  • 3 eggs, lightly beaten
  • 1/4 cup olive oil
  • 1/2 cup honey
  • 1/2 teaspoon baking soda
  • 1/4 cup coconut flour
  • 1/4 cup cocoa powder
  • 1/3 cup flaxseed, ground
  • 1/2 cup gluten-free chocolate chips
  • Additional flaxseed (optional topping)


Preheat oven to 375 degrees F. Stir together eggs, olive oil, and honey. Whisk in baking soda, then coconut flour. Add cocoa powder and ground flaxseed and mix thoroughly. Stir in chocolate chips.

Prepare muffin pan with cooking spray or muffin cup papers. Spoon batter into muffin pan, filling each cup about 2/3 full. Bake for 8-10 minutes (mini-cupcakes) or 18-20 minutes (regular cupcakes). Remove from oven and allow to cool for 5 minutes. Remove from muffin pan and cool completely on wire rack.

Note: If garnishing with flaxseed, sprinkle on top of each muffin after 5 minutes of baking to prevent flaxseed from sinking into batter.

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  1. I love what you did with these!! I am officially signed up for Recipe ReDux but did it late this month, so didn’t have time to cook something up…can’t wait for next month though!

    1. Can’t wait to see what you come up with! πŸ™‚

  2. I’m thinking when I get home I will be grinding up some flaxseed to make these, they look delicious!

  3. I would love to eat one of these…right now πŸ˜‰ They look scrumptious!

  4. Smile. I love stacking my cupcakes and muffins. Silly but so pleasing when it works! I must say that I loved seeing the fallen ones too! These look so good Jessie (and good for you too!) Maybe I’ll get a batch in before Lucy comes!

  5. Two double chocolate thumbs up!

  6. Happy birthday to me! (: It’s my birthday tomorrow and I’m totally making these for myself! They look amazing. OK, not to be cheeky, but cacao powder the same as cocoa powder?

    1. Happy Birthday, Serena! I hope you have a wonderful day πŸ™‚

      Thanks for catching cacao vs. cocoa! I meant cocoa, although I think they’re interchangeable. I’ll correct it in the recipe right now.

  7. Thanks so much for the recipe! Just sent it along to my mother. These are delicious–the texture was moist and delicate, and the flavor was just the right blend of chocolate with the faint nuttiness from the flax. I particularly liked having a single chocolate chip on top–that extra burst of chocolate really “took the cake.”

    1. Why, thank you, my good lady πŸ™‚

  8. Hee hee, I feel the same way about cupcakes/muffins (frankly, they’ll never go out of style.) Definitely want to try this recipe as I love using ground flaxseed in my cupcakes/muffins – think by 6 yr old daughter will love these!

  9. OK – we just made these this morning (I added a little bit more flour for girth) and they were DELICIOUS!!! Even my picky eating husband ate them πŸ™‚

    1. Yay, I’m so glad you liked them! πŸ™‚

  10. I didn’t have eggs so I created flaxseed eggs, also replacing the flaxseed in the recipe with LSA. They are very moist! πŸ™‚ Thank you!

    1. Hi Betty, so glad you liked them! πŸ™‚

  11. Hi Jessie πŸ™‚
    Somehow I came across this three year old blog post of yours and decided to try this – first gluten free cupcakes not from a box-mix! I exchanged the flax seeds for shredded coconut (yes, MORE coconut) and they are pretty good, except a tiny bit dry – must be the extra coconut. Should I add a little milk next time? Definitely making these again! πŸ™‚
    Hope you and the little one are doing great!

    1. Hi Sandi! Mmm, coconut πŸ™‚ Definitely try a little milk next time, or a little more olive oil will make the recipe even more moist.

      Thanks for the good wishes! We are doing well!

  12. I tried to make these cupcakes last night. They were very Moises and liked great but tasted and smelled burnt. Why do you think that?

    1. Hi Quin, thanks for your comment! It’s hard to say why the taste and smell were off. Flax has an earthy flavor, and the taste of the flax might have been too strong (especially if it had turned). Also, this recipe is low in sugar, which brings other flavors out. If you’d like to try again, I’d recommend starting with fresh flax seed, perhaps adding a little less, and if you’d like a sweeter taste, add a little more honey or fruit puree.

      Hope that helps!

  13. So sorry about typos….they were moist and looked great

  14. Hi Jessie, Do you think I can use egg whites in place of eggs and tapioca flour in place of coconut. I have a niece with allergies.

    1. Hi Mindy! You can definitely use egg whites instead of eggs–use two egg whites or 1/4 egg white in place of one egg. The tapioca flour is a little trickier. Coconut flour is really absorbent, so you might find the batter to be really liquidy without it. You may need to add more flour than the recipe calls for to keep it from being too liquidy. Alternatively, you can cut down on the amount of liquid ingredients, although then you’d have fewer cupcakes, and who wants that? πŸ˜‰

      Good luck!

  15. I made these this evening for my daughter who is gluten free, dairy free, and soy free. These are fantastic and she was so excited to have a very tasty treat with all allowed ingredients!

    1. I’m so glad you enjoyed them πŸ™‚

  16. I added vanilla and sea salt and used tapioca flour instead of coconut because my daughter is allergic but sooo good and every thing was organic delicious thank you

    1. So glad you liked them!

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