Apple Crumb Muffins (Paleo, Gluten-Free)

These paleo apple crumb muffins are soft and moist with juicy apples, warm cinnamon and a buttery crumb topping. Gluten-free and dairy-free.

These apple crumb muffins are soft, moist, and packed with fresh apple flavor, warm cinnamon, and the best buttery crumb topping!

They have tender almond flour-based muffins underneath and plenty of cinnamon crumble on top for that bakery-style apple muffin feel.

I use both grated and diced apples in the batter. The grated apple melts into the muffins as they bake to keep them moist, while the diced apples give you juicy apple pieces in every bite!

These muffins are naturally gluten-free, grain-free, dairy-free, and paleo-friendly, and they’re perfect for fall breakfasts, snacks, or whenever you’re craving apple cinnamon everything!

Why You’ll Love These Apple Crumb Muffins

There’s a lot going on in these muffins in the best possible way: a tender cinnamon-spiced muffin, two kinds of apple texture, and a thick layer of buttery crumble.

They’re also easy to make in one muffin pan and don’t require any complicated techniques!

A few things that make this recipe especially good:

• Lots of fresh apple: Grated apple adds moisture while diced apple gives you distinct juicy bites.
• Soft almond flour texture: Just 2 tablespoons of coconut flour are used, so these muffins don’t have a dry or overly coconut-flour-heavy texture.
• Generous crumb topping: The cinnamon almond flour crumble gives these muffins that bakery-style finish.
• Naturally gluten-free: Almond flour, tapioca flour, and coconut flour create the perfect grain-free flour blend.
• Dairy-free and paleo-friendly: Refined coconut oil keeps both the muffins and crumb topping dairy-free.

The Best Apples for Apple Muffins

Firm, flavorful baking apples work best because you want the diced apples to soften without completely disappearing into the batter.

My favorites are Honeycrisp and Granny Smith, and I especially like using a combination of the two. Honeycrisp adds sweetness and great apple flavor, while Granny Smith adds a tart contrast and holds its shape well during baking.

Pink Lady, Braeburn, or Fuji are also good options!

Avoid very soft apples, which can release too much moisture and lose their texture as they bake.

Why Use Both Grated and Diced Apples?

Using the apples two different ways gives these muffins a much better texture than using only diced apples.

The grated apple blends into the batter and adds moisture and apple flavor throughout the entire muffin. Lightly squeezing out the excess liquid prevents the batter from becoming too wet.

The diced apple gives you those juicy, noticeable apple pieces you want in an apple muffin.

Don’t squeeze the grated apple completely dry. Just gently remove the excess moisture before measuring it into the batter.

Ingredients and Substitutions

Almond Flour

Use blanched almond flour, not almond meal. Almond meal is coarser and can make the muffins heavier and more crumbly.

Tapioca Flour

Tapioca flour helps give the muffins structure and a lighter texture that balances the almond flour. Arrowroot flour can be substituted in the same amount.

Coconut Flour

Only 2 tablespoons are needed. Coconut flour absorbs some of the moisture from the apples without dominating the texture of the muffins.

Because coconut flour behaves very differently from other flours, I don’t recommend replacing it with additional almond or tapioca flour without testing.

Maple Sugar

I prefer maple sugar for its mild caramel flavor, but coconut sugar works well too.

Refined Coconut Oil

Refined coconut oil keeps the muffins dairy-free without adding a noticeable coconut flavor.

Almond Milk

Only 1/4 cup is needed because the eggs and apples already provide plenty of moisture.

Any unsweetened dairy-free milk with a similar consistency should work.

How to Make Apple Crumb Muffins

Make the cinnamon crumb topping

Combine the almond flour, maple sugar, cinnamon, and salt. Work the softened coconut oil into the dry ingredients with a fork until crumbs form.

Don’t mix until completely uniform. You want a combination of smaller crumbs and larger clusters.

Chill the crumble while you prepare the muffin batter. Keeping it cold helps the crumbs hold their shape while baking.

Prepare the apples

Peel the apples before grating and dicing them.

Coarsely grate enough apple to measure 3/4 cup, then lightly squeeze out excess moisture.

Finely dice enough additional apple to measure 1 cup.

Mix the muffin batter

Whisk the dry ingredients together in one bowl.

In a separate large bowl, whisk the eggs, almond milk, maple sugar, coconut oil, vanilla, and lemon juice until smooth, then stir in the grated apple.

Stir the dry ingredients into the wet ingredients just until combined.

Allow the batter to rest for about 2–3 minutes so the coconut flour has time to absorb some moisture, then gently fold in the diced apples.

Add the crumble and bake

Divide the batter evenly among 12 lined muffin cups. The cups should be fairly full.

Generously crumble the chilled topping over the muffins. Make sure to include some of those larger crumb clusters on each muffin.

Bake at 350°F until the tops are set and a toothpick inserted into the center comes out clean or with a few moist crumbs.

Tips for the Best Apple Crumb Muffins

Measure the apples after preparing them. Apples vary enormously in size, so measuring the grated and diced apples gives you much more consistent results than simply calling for two apples.

Don’t over-squeeze the grated apple. You want to remove obvious excess liquid without removing all of its moisture.

Let the batter sit for a few minutes. Coconut flour absorbs liquid quickly, and this short rest allows the batter to reach its final consistency before you fill the muffin cups.

Keep the crumble cold. If the coconut oil becomes too warm, the crumb topping is more likely to melt into the muffins rather than forming distinct clusters.

Don’t overbake. Almond flour muffins continue to firm up as they cool. Remove them once a toothpick comes out clean or with just a few moist crumbs.

Allow them to cool before serving. The texture improves significantly as the muffins cool and set.

Optional Vanilla Glaze

These apple crumb muffins don’t need a glaze, but a light vanilla drizzle is delicious if you want a sweeter, bakery-style finish!

For a paleo-friendly glaze, whisk together:

• 1/2 cup powdered maple sugar
• 1 tablespoon unsweetened almond milk, plus more as needed
• 1/2 teaspoon pure vanilla extract
• Tiny pinch fine sea salt

Add just enough almond milk to create a glaze thick enough to drizzle in ribbons over the cooled muffins.

I recommend keeping the drizzle light so the cinnamon crumb topping is still visible.

How to Store Apple Crumb Muffins

Once completely cooled, store the muffins covered at room temperature for about a day.

For longer storage, refrigerate them in an airtight container for up to 5 days.

Because almond flour baked goods firm up when chilled, I recommend allowing a refrigerated muffin to sit at room temperature before serving or warming it briefly.

Can You Freeze Apple Muffins?

Yes. Allow the muffins to cool completely, then place them in a freezer-safe container or bag and freeze for up to 2–3 months.

For the best appearance and texture, I recommend freezing the muffins without the optional glaze and adding it after thawing.

Thaw overnight in the refrigerator or at room temperature before serving.

Frequently Asked Questions

Are these apple crumb muffins gluten-free?

Yes. These muffins are made with almond flour, tapioca flour, and coconut flour, so they’re naturally gluten-free and grain-free.

Are these muffins paleo?

Yes, when made with paleo-friendly ingredients such as maple sugar or coconut sugar and refined coconut oil.

Can I substitute arrowroot for tapioca flour?

Yes. Arrowroot flour can be substituted for the tapioca flour in a 1:1 ratio in this recipe.

Do I have to peel the apples?

I recommend peeling them. Apple peel can stay slightly chewy in muffins and interfere with the soft texture, especially in the diced apple pieces.

Why do I need to squeeze the grated apple?

Removing some excess liquid prevents the muffin batter from becoming overly wet. However, don’t squeeze the grated apple completely dry because some of that moisture helps keep the muffins tender.

Can I make these without the crumb topping?

You can, but I highly recommend keeping it. The cinnamon crumb topping is one of the best parts of these muffins and gives them much more texture and flavor.

Can I leave off the vanilla glaze?

Absolutely. The muffins are designed to be delicious without glaze. The drizzle is simply an optional bakery-style finishing touch.

These paleo apple crumb muffins have everything I want in a fall muffin: plenty of fresh apple, warm cinnamon, a soft and moist crumb, and a generous buttery crumble topping.

They’re easy enough for everyday baking but feel special enough for a weekend breakfast or fall brunch. Add a little vanilla glaze for a bakery-style finish, or enjoy them straight from the cooling rack with all that cinnamon crumble on top.

I hope you’re ready to bake – let’s go!

More Paleo Apple Recipes:

Paleo Apple Pie Bars 

Spiced Apple Cider Muffins

Apple Crumb Cake

Apple Cobbler

Glazed Apple Bundt Cake

Paleo Apple Pie 

Apple Crumb Muffins (Paleo, Gluten-Free)

These paleo apple crumb muffins are soft and moist with juicy apples, warm cinnamon and a buttery crumb topping. Gluten-free and dairy-free.

Author: Michele

Prep Time: 20 minutes

Cook Time: 25 minutes

cooling time: 30 mins

Course: Breakfast/brunch, Dessert/Snack

Cuisine: dairy-free, Gluten-free, grain free, Paleo

Servings: 12 muffins

Print this Recipe

Did you make this recipe?

Leave a review

4.67 from 87 votes

Ingredients

Cinnamon Crumb Topping:

• 1/2 cup blanched almond flour
• 1/4 cup maple sugar or coconut sugar
• 1 teaspoon cinnamon
• Pinch fine sea salt
• 3 tablespoons refined coconut oil softened but not melted

Apple Muffin Batter:

• 2 cups blanched almond flour
• 1/2 cup tapioca flour or arrowroot flour
• 2 tablespoons coconut flour
• 1 1/2 teaspoons cinnamon
• 1/4 teaspoon nutmeg
• 1 teaspoon baking powder
• 1/2 teaspoon baking soda
• 1/2 teaspoon fine sea salt
• 4 large eggs room temperature
• 1/4 cup unsweetened almond milk
• 2/3 cup maple sugar
• 1/4 cup refined coconut oil melted and cooled
• 1 1/2 teaspoons pure vanilla extract
• 1 tablespoon fresh lemon juice
• 3/4 cup peeled coarsely grated apple, lightly squeezed to remove excess moisture
• 1 cup peeled apple finely diced

Vanilla Glaze:

• 1/2 cup powdered maple sugar or powdered sugar
• 1 tablespoon almond milk
• 1/2 teaspoon vanilla
• Tiny pinch salt

Instructions

1. Preheat your oven to 350°F and line a 12-cup muffin pan with parchment liners.
2. In a small bowl, combine the almond flour, maple sugar, cinnamon, and salt. Add the softened coconut oil and use a fork to work it into the dry ingredients until a crumbly mixture forms. You want a combination of smaller crumbs and larger clusters. Place the crumb topping in the refrigerator while you prepare the muffin batter.
3. Peel the apples. Coarsely grate enough to measure 3/4 cup, then lightly squeeze the grated apple with your hands or a paper towel to remove excess liquid. Don't squeeze it completely dry.
Finely dice enough additional apple to measure 1 cup. Set aside.
4. In a medium bowl, whisk together the almond flour, tapioca flour, coconut flour, cinnamon, nutmeg, baking powder, baking soda, and salt.
5. In a large bowl, whisk the eggs, almond milk, maple sugar, melted coconut oil, vanilla, and lemon juice until smooth and well combined.
Stir in the grated apple.
6. Add the dry ingredients to the wet mixture and gently stir until just combined and no dry flour remains. Allow the batter to sit for 2–3 minutes so the coconut flour can begin absorbing moisture. Fold in the diced apples. The batter should be thick and scoopable but still moist, not stiff like dough.
7. Divide the batter evenly among the 12 prepared muffin cups. They should be fairly full.
Remove the crumb topping from the refrigerator and crumble it generously over each muffin. Use all of the topping, leaving some larger pieces intact.
8. Bake in the preheated oven for 22–26 minutes, or until the muffin tops are set and a toothpick inserted near the center comes out clean or with a few moist crumbs.
9. Allow the muffins to cool in the pan for about 10 minutes, then carefully transfer them to a wire rack to cool completely.
10. For the vanilla glaze, mix ingredients together in a small bowl until smooth, adding milk slowly. Drizzle the muffin tops with glaze after they’ve cooled.

Recipe Notes

Once completely cooled, store the muffins covered at room temperature for about a day.

For longer storage, refrigerate them in an airtight container for up to 5 days.

Because almond flour baked goods firm up when chilled, I recommend allowing a refrigerated muffin to sit at room temperature before serving or warming it briefly.

Nutrition

Calories: 313kcal

Carbohydrates: 28g

Protein: 7g

Fat: 21g

Saturated Fat: 8g

Polyunsaturated Fat: 0.5g

Monounsaturated Fat: 1g

Trans Fat: 0.01g

Cholesterol: 55mg

Sodium: 198mg

Potassium: 137mg

Fiber: 3g

Sugar: 17g

Vitamin A: 98IU

Vitamin C: 2mg

Calcium: 105mg

Iron: 2mg

Did you make this recipe?

Tag @PaleoRunningMomma on Instagram and hashtag it #PaleoRunningMomma