apple flax muffins

$3.49 recipe / $0.29 serving
by Beth - Budget Bytes
4.89 from 9 votes
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I’m really not one to use all sorts of fancy “health food” ingredients but strangely enough, I enjoy the flavor and texture of things like bran and flax meal. So, when I spotted a box of flax meal at the store for less than $3, I grabbed it. I love to sprinkle the stuff on my oatmeal or in my yogurt.

On the back of the box I found this recipe for apple flax muffins. I thought it looked interesting and it kind of reminded me of the morning glory muffins that I made and loved so much… except even healthier.

Well, I switched around some ingredients, made a couple of substitutions and came up with a version all my own. Flax seed contains a bunch of good fat so it wasn’t necessary for any extra oil to be added to the batter. The texture of the batter is definitely different (a little stiff/gooey) and I almost thought the recipe was going to be a flop, but while they were in the oven magic happened. They puffed up and turned into delicious, light, yet hearty muffins!

After they cooled, I zipped them up tight in a freezer bag and popped them into the freezer. Now I can pull out one muffin at a time, thaw it in the microwave for 30 seconds and enjoy the yummy muffin goodness whenever I want!

Apple Flax Muffins

Apple Flax Muffins on cooling rack

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Apple Flax Muffins

4.89 from 9 votes
A muffin that is truly healthy enough to be called breakfast. These apple flax muffins are chock full of fiber and not overly sweet, yet still delicious.
Servings 12
Prep 15 minutes
Cook 20 minutes
Total 35 minutes


  • 1 3/4 cups whole wheat flour ($0.28)
  • 3/4 cup ground flaxseed ($0.27)
  • 2 tsp baking soda ($0.08)
  • 1/2 tsp baking powder ($0.02)
  • 1/2 tsp salt ($0.02)
  • 1/2 tsp cinnamon ($0.02)
  • 1/2 cup brown sugar ($0.16)
  • 1 large egg ($0.18)
  • 1/2 cup unsweetened applesauce ($0.25)
  • 1/2 cup plain non-fat yogurt ($0.25)
  • 1/2 tsp vanilla extract ($0.14)
  • 2 medium apples ($1.81)
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  • Preheat the oven to 400 degrees. In a large bowl combine the dry ingredients (flour, ground flax seed, baking soda, baking powder, salt, and cinnamon).
  • In a medium bowl, whisk together the wet ingredients (egg, brown sugar, yogurt, apple sauce, and vanilla). Core and chop the apples into small pieces.
  • Pour the wet ingredients into the bowl of dry ingredients. Stir just until combined. Fold in the chopped apples just until they are evenly distributed. Try not to over stir the mixture or else the muffins may become tough or rubbery.
  • Spray a muffin tin with non-stick spray or line with paper cups. Evenly distribute the muffin batter between 12 muffin cups. Bake in the preheated 400 degree oven until golden brown and a toothpick inserted in the center comes out clean (about 20-25 minutes). Remove the muffins from the tin and let cool on a wire rack.

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Serving: 1ServingCalories: 164.47kcalCarbohydrates: 29.73gProtein: 4.73gFat: 4.02gSodium: 341.03mgFiber: 4.66g
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apple flax muffin cut in half and placed on white plate

Step By Step Photos

flax seed meal in package
This is the ground flax seed that I bought. I put it on just about everything. Flax seed meal, ground flax seed and milled flax seed are all the same thing. Because of the delicate omega-3 fatty acids, it needs to be kept in the refrigerator once opened.

dry ingredients in mixing bowl
In a large bowl, combine the dry ingredients: flour, ground flax seed, baking powder, baking soda, salt, and cinnamon. Because of the way it dissolves, we’re counting brown sugar as a wet ingredient. Oh, go ahead and start preheating the oven to 400 degrees.

wet ingredients in mixing bowl
In a smaller bowl, whisk together the wet ingredients: brown sugar, egg, apple sauce, yogurt, and vanilla.

mixed wet ingredients in mixing bowl with whisk
It will look a little something like this.

two apples with knife
Before you combine the wet and dry, make sure you have your apples ready. You can use any type of apple depending on how sweet you like things. I used gala apples which are a little on the sweet side, but there isn’t much sugar in the batter so they worked well.

chopped apples
Core and chop the apples. I left the skin on but that’s up to you. Next time I think I’ll cut the apples a bit smaller. The long rectangles weren’t that visually appealing.

combining wet ingredients to dry ingredients
Now it’s time to combine the wet and dry ingredients. Pour the wet into the dry and stir just until everything is moist and then fold in the apples. Try not to over stir.

muffin batter with chopped apples
This is what my batter looked like. It was a little thick and I had to scoop it into the muffin tin rather than pouring like a regular muffin batter. I was worried, but once it was in the oven everything turned out okay.

muffin tin filled with batter
Fill the muffin cups all the way up to the top (or just divide the batter evenly among the 12 cups). Place them in the preheated oven and bake until they’re nice and brown on top (about 20-25 minutes).

baked muffins in muffin tin
I was really pleased with how well they rose once in the oven. I thought for sure the batter was too thick to yield a nice fluffy muffin but I was wrong. I guess the flax meal just creates a different texture in the batter.

Close up of apple flax muffins in muffin tin
Take the muffins out of the tin and allow them to cool. If left in the muffin tin to cool, steam will cause the bottoms to get soggy. Soggy muffins = sad muffins.

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  1. Really nice recipe and easy instructions. Had alot of flax seed and had to use it up….will definitely make this again. Thanks for sharing it with us❤

  2. I’d like to make these for breakfast for myself for a whole week. Do they last well on the counter (or in the fridge, if necessary), or do they dry out fast? Also, have you tried making a double batch and freezing them?

    1. They will last about a week in an air-tight container. I would not recommend storing them in the fridge because that will likely dry them out. For freezing, I’d suggest using a similar technique for preparing the cake layers of an ice cream cake. (Although, to be honest, I haven’t tested this method with this specific recipe, so I’m not totally sure it will be successful. I’d maybe store half in the pantry and try freezing the other half, just to be safe.) I’m not quite sure how long they would stay good frozen, but I’d suggest trying to eat them within 1-2 weeks.

      Here’s what I’d do:
      – Remove the muffins from the oven and let them cool for about 10 minutes (cool enough to touch the pan without burning yourself), and then wrap the tray with plastic wrap, and freeze it. This will help lock the moisture into the crumb.
      – Once cold to the touch (about 30 min or so), take the tray out of the fridge and individually wrap each muffin with plastic wrap and transfer to a freezer bag.
      – Thaw in the fridge overnight, on the counter, or remove the plastic wrap and toast lightly in the oven/toaster oven.

      ~ Marion :)

  3. Followed the recipe exactly and had perfect apple flax muffins! Incredibly delicious and not dense n chewy like I feared. Thanks for another winner!!

  4. I visit A LOT of recipes sites. Your’s is site is one of the best.
    I love the idea of giving approximate cost of ingredients.
    There’s probably a way to make the prices dynamic and total on screen.
    The recipe is clear and easy to find on the page, which is not always the case.

  5. This recipe is wonderful and easy😊. Also really appreciate that you can skip right to recipe without all the adds and clutter that Zi have experienced from other recipes. Thank you so much. 

  6. I had to add a tablespoon or two of water because the batter was too dry. The batter will be very dense still but it does bake nice. I used half the sugar and they taste sweet enough for my palate. They are very yummy and I smothered some coconut oil on each half. Each muffin gives you a tbsp. serving of flax meal. I try to eat two tbsp. a day mixed in water but this way I get to enjoy two muffins to reach that amount. Thank you for sharing and God bless you!

    1. It uses whatever name you enter on the form, but no problem, I am able to change it for you. :)

  7. I made several changes since I am not fond of wheat flour so to make up the bulk added 1 scoop veg. Protein, 1/2 c oats,.cut sugar by half and used brn.sugar. this made mo visible difference THE MUFFINS ARE FANTASTIC. Even found my cat sitting in front of oven for the first time in 7 years.

  8. These were very easy to make. I used greek yogurt bc I didn’t have reg. and compensated for the reduced moisture in the greek by adding a mashed banana. These were DELISH! Anddd a healthy breakfast option jam packed with fiber! Speaking of… they are extra yummy topped with some honey, jam or almond butter. THANK YOU FOR THIS RECIPE!