These sweet, tender and moist Paleo Apple Muffins have a deliciously addicting coconut sugar and cinnamon crumb topping and juicy apples throughout. They’re grain free, paleo, dairy-free, gluten-free, easy to make and family approved!
Have you gone apple picking yet?! I have not. When the kids were babies, it wasn’t hard to “schedule” in apple picking as soon as September rolled around. In fact, there were years I went twice, if only to have some sort of activity to get us all out of the house with strollers, diapers, and all that other jazz in tow.
It sort of amazes me now that I went through all that trouble for apple picking, because now (and since the kids have been school-age) it stresses me out just trying to find a free day to apple pick before October slaps me in the face and the apples are gone.
Between birthday parties, friend/family get-togethers and other random stuff that I can’t even pinpoint, apple picking has been demoted way down on the priority list.
The apple picking struggle is real, here, as I’m sitting here making mental calculations of how many chances we even have before the month is over. And hasn’t it only just begun?!
I mean, if my calculations are correct, and assuming my mind isn’t completely gone, wasn’t it just Labor Day Weekend? It definitely doesn’t help that I’ve been testing apple recipes for a solid month and a half now (eek!) and pumpkin ones for almost as long. I want my FALL back!!
Anyway, let’s slow down, savor the moment, and also savor the flavor of these paleo apple muffins. Yes I’m 100% aware that my last sentence sounded silly. Would sava-the-flava be better? No, no again, and nope, it would not.
Of course now I’ll be saying all day since I made such a big deal of it. But anyway, the muffins! Apple muffins are a must-make in the fall, whether you pick your own apples or not. I oddly did not have a paleo version until just now, even though I had lots of other apple recipes on the blog. Now, forgive me as I channel Bubba (Forest Gump) and list a few:
Apple pie skillet cookie, apple crisp, apple pie bars, apple cinnamon pancakes, caramel apple coffee cake, sweet potato apple breakfast bake, apple cinnamon hot cereal, sautéed apples and pears, and more to come. The muffins needed to be here, don’t you think?
So here we have it – classic apple muffins with a delicious cinnamon crumb topping that also happen to be grain free, dairy free, and paleo.
The muffins are moist and tender, thanks to doubling up on the apples (shredded and diced!) and they’re packed with all that spicy sweet fall flavor we love. You won’t want to say no to this! And, since they’re easy to make and actually good for you, it’s all YES for these paleo apple muffins!
One note on the coconut oil I used for this recipe (and for most of my baking recipes.) I usually stick with organic refined coconut oil for baking, as opposed to extra virgin, since refined is 100% flavorless, so you don’t get that “weird paleo taste” that kids and non-paleo eaters will tend the notice before they even take a bite.
I, personally, don’t mind the taste of coconut in nearly anything, but, for many of you feeding kids and other family members who are new to paleo, going with the refined coconut oil ensures you minimize coconut flavor and allow the other flavors to shine through.
That said, if you’d prefer to stick to extra virgin, it will work just fine! Are you ready to bake? Let’s go!
Paleo Apple Muffins with Crumb Top
Paleo Apple Muffins with Crumb Topping

Ingredients
Crumb top:
- 5 tbsp almond flour
- 2 tbsp coconut oil soft
- 3 tbsp coconut sugar
- 1.5 tsp cinnamon
- Pinch sea salt
Muffin Batter:
- 4 eggs
- 1/4 cup almond milk unsweetened, or other dairy-free milk you prefer
- 6 tbsp coconut sugar
- 3 tbsp coconut oil
- 1 med/large apple peeled and shredded, excess water squeezed out
- 1 1/2 tsp pure vanilla extract
- 1 tbsp fresh lemon juice
- 1 cup blanched almond flour
- 1/4 cup coconut flour
- 1/3 cup tapioca flour
- 2 tsp cinnamon
- 1/2 tsp nutmeg
- 1/4 tsp sea salt
- 1 tsp baking soda
- 1 med/large apple peeled and finely diced
Instructions
-
Preheat your oven to 375 degrees F and line a 12 cup muffin pan with parchment liners*
-
Combine crumb mixture ingredients in a bowl with a fork until combined (it should look like crumbs) then chill while you prepare muffin batter.
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Combine dry ingredients in a medium bowl, except the coconut sugar, and set aside.
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Whisk together eggs, almond milk, vanilla, sugar, grated apple, coconut oil and lemon juice in a large bowl until well combined
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Gently stir dry ingredients into wet until no flour spots show, then fold in finely diced apples.
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Scoop into 12 lined muffin cups evenly and sprinkle the chilled crumb topping over each one. Bake in preheated oven 15-20 mins or until muffins rise and toothpick inserted into center of one muffin comes out clean. Allow to cool completely on wire racks before serving. Enjoy!
Nutrition
What I Used To Make My Paleo Apple Muffins with Crumb Topping:
Want More Paleo apple recipes? Try one of these!
Maple Pecan Apple Crisp {Paleo and Vegan}
Paleo and Vegan Apple Pie Bars
Sautéed Apples and Pears with Coconut Butter {No added sugar}
Sweet Potato Apple Breakfast Bake {Whole30}
Tell Me!
Do you go apple picking every year? First thing you make after?
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My whole family enjoyed these! I’ve made quite a few of your savory recipes, but since we recently discovered two of my kids have celiac I have been really grateful to learn gluten-free baking from you. We have liked your recipes better than those made with “cup-for-cup” type flours!
Can pears replace apples in this recipe? If so what modifications need to be made? Thanks!
Made these today and they turned out very greasy, not sure what I did wrong.
I actually made these for our Airbnb guests! If people are not used to clean eating, they may think they are bland without all the sugar, however, for me being a clean eater, I thought they were amazing. Moist and flavorful!
Added some pumpkin purée and ground flax seeds, since I had some left over. Also used Vanilla Hemp milk. They turned out perfectly!
Hi. Thanks for a great recipe. Please, can arrowroot powder be substituted for the tapioca flour. Can’t wait to try your recipe! Thanks again!
I have these in the oven right now and they smell heavenly! Can’t wait to try them. What do you recommend for storing them if they won’t all be eaten right away? Thanks!
I plan on making these Saturday morning. Do you think I could assemble the ingredients the night before ? Maybe I will add the apples that morning so they don’t oxidize? Your thoughts are appreciated
Just made these for my 2 y.o. grand daughter. I halved the sugar and only put in 1/2 teaspoon of cinnamon. No topping. I used mini muffin pan size. In the freezer now, ready for snacks.
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Hi! I have some apples that I cooked down already. Could I use them in the recipe as is and just replace the raw apple? What would be the measurement? (i.e. 1 cup? etc). I love your recipes I make them all the time 🙂