Cherry Chia Mini Muffins

June 11th, 2013 at 6:06 am

It’s been a while since I’ve shared a new muffin recipe. I’ve been waiting for inspiration to strike, and it just so happened to hit me when I spotted some beautiful fresh cherries at the store the other day. I wasn’t in the mood for anything big and cakey, so I decided to make little mini muffins instead with coconut flour so that they’d be nut-free.

These muffins are definitely more on the moist and eggy side than the crumbly and cakey side, which is just what I was after. They are a high-protein treat to enjoy for breakfast (perfect with a smoothie!) or as a light afternoon snack. Skipping the starchier flours makes for a mini muffin that won’t weigh you down or make you take a carb crash.

Chia seeds enrich these beauties with healthy fats and fiber. I’ve been throwing them in everything lately, it seems. Smoothies, on top of salads, even in hot cooked foods. You don’t even taste them, I promise! So much great nutrition in such a tiny and flavorless package.

Truth be told, I haven’t been in the kitchen much lately. This time of year, I find myself so enticed by the warmer weather that whenever I have a spare minute I would rather go outside than stand in the kitchen and cook. That said, when I am taking the time to prepare wholesome food, I want to be in and out of the kitchen quickly and easily. I like having treats like these on hand for quick grab and go fuel straight from the fridge.

Substitution Options

  • Eggs: Sorry, but substituting something else for the eggs won’t work here. They are vital to the structure and texture of the muffins.
  • Honey: Try maple syrup or coconut nectar in an equal amount.
  • Coconut flour: The coconut flour is kind of the “backbone” of this recipe, so I’m afraid you can’t replace it with a suitable substitute unless you change many other aspects of the recipe.
  • Cherries: Try other fruits like chopped peaches, strawberries, or blueberries. Whatever is your favorite or inspires you!

More healthy baked treats for summer snacking:

Cherry Chia Mini Muffins

Yield: Makes 12 mini muffins

These delightful little muffins make the perfect breakfast treat! If you don't have cherries on hand, use blueberries or chopped strawberries or peaches instead.


3 large eggs, room temperature

1/4 cup unsweetened applesauce

3 tablespoons honey

2 tablespoons virgin coconut oil, melted

2 tablespoons ground chia seeds

1 tablespoon finely grated lemon zest

1 teaspoon vanilla extract

1/4 cup (29 grams) coconut flour

1/2 teaspoon baking soda

1/2 teaspoon ground ginger

Pinch of sea salt

1/2 cup pitted and chopped sweet cherries


Preheat the oven to 350ºF. Line 12 cups of a mini muffin pan with paper liners.

In a food processor, puree the eggs, applesauce, honey, coconut oil, ground chia seeds, lemon zest, and vanilla until smooth. Add the coconut flour, baking soda, ginger, and salt. Puree until smooth.

Divide the batter among the lined muffin cups. (The cups will be pretty full and may rise a little over the edges of the pan in the oven. I didn't mind this, but If you'd like less full muffin cups, make 14-15 mini muffins instead.)

Press a few chopped cherry pieces gently into the batter of each muffin. Bake for 18-20 minutes until deeply golden brown and a toothpick inserted comes out clean. Cool completely before removing from the pan. Store in an airtight container in the refrigerator.



  1. Such a GREAT idea to post substitution notes Hallie! I’ve never tried cherries in muffins. We won’t get ours until August so I will try some then :)

  2. Love the flavor idea and mini muffin approach with these Hallie. I really need to get a mini muffin tin!

  3. These are just gorgeous, Hallie. And so fresh and healthy. Cannot wait to try these! :D

  4. Just made these and they came out fantastic. I noticed when it was too late that the recipe called for ground chia seeds and made mine with whole chia seeds – but I love chia so it did not bother me. They came out a bit like lemon poppy. Hallie – I just bought your cook books from Amazon and have been making a bunch of your recipes – the pizza crackers (yum!) and several others. Thanks so much!

  5. My first success at coconut flour baking!

    This is now my stand-by, perfect GF muffin/ baked item to prove that gluten free is awesome.

    I admit that I added more chopped cherries into the batter for my 2nd batch because I’m addicted to them– even though that batch became a bit more spongy from the extra liquid, they tasted just right!

  6. Theresa P. said on August 8, 2013 at 5:54 pm

    Oh! these look and sound so delish! I am going to add some almond extract to intensify the cherry flavor. and I think I might also add some chocolate chips/chunks. I love cherry and chocolate together. Thanks, for sharing.

  7. Damiane said on July 9, 2015 at 8:37 am

    I’mout of lemon to make the zest. Is there a substitute or is it crucial to the recipe?

Leave a Reply

The Pure Kitchen Books

In Hallie’s cookbooks you’ll find gluten-free, dairy-free recipes made with whole, natural foods.

The Pure Kitchen: Amazon | Hallie's eStore

Super Healthy Cookies: Amazon | Hallie's e-store

Dairy-Free & Gluten-Free: A Whole Food Starter Guide and Cookbook

About me

I'm Hallie Klecker, a professional recipe developer, author, and passionate gluten-free foodie. As a certified holistic nutrition educator, my goal is to inspire others to live a balanced, nourished life through eating well and living pure—one bite at a time. Learn more.