Gluten-Free Apple Muffins Recipe for Moist, Flavorful Bites

These gluten free apple muffins are easy to make, studded with sweet apple chunks and topped with a crunchy cinnamon streusel topping.

Three muffins stacked on top of each other, on a wooden board, with an apple and small dish of cinnamon in the background, text overlay reads "gluten free apple muffins".

I love simple, reliable baking recipes, and these gluten-free apple muffins are just that — a quick way to bake a moist, flavorful breakfast or snack. They’re studded with juicy apple pieces and finished with a crunchy cinnamon-brown sugar crumble.

If you’ve ever had dry gluten-free muffins, don’t worry. The apple chunks and a touch of thick plain yoghurt keep these muffins tender and moist.

Half of a gf apple muffin, showing the texture of the muffin and the chunks of apple inside.

What You’ll Love About These Gluten Free Apple Muffins:

Delicious chunks of apple – juicy pieces throughout each muffin.
Cinnamon crumble topping – a sweet, crunchy finish.
Lightly spiced – warm cinnamon notes, subtle and comforting.
Easy to make – a classic melt-and-mix muffin method.

Ingredients

Apples – any juicy eating apple will work (Braeburn, Pink Lady, Gala, Granny Smith). You’ll need about 2 medium apples (approx. 200g chopped).
Gluten free flour – use your preferred gf all-purpose blend (note: results vary by blend).
Xanthan gum – include only if your flour blend doesn’t already contain a gum.
Baking powder – ensure it’s gluten free.
Cinnamon – ground cinnamon for warmth; add a pinch of nutmeg or mixed spice if you like.
Brown sugar – light or dark both work.
Butter – salted or unsalted (add a pinch of salt if unsalted).
Milk – whole milk preferred, but low-fat is fine.
Plain thick yoghurt – Greek-style unsweetened yoghurt keeps the muffins moist (sour cream may also work).
Egg – one large egg.
Vanilla – vanilla extract or vanilla bean paste (optional).

How to Make Gluten Free Apple Muffins

For full measurements and timings see the recipe card below.

Prepare the muffin tin

Grease a 12-hole muffin pan with oil spray or melted butter, or line with paper cases.

Make the crumble topping

Combine the gf flour, brown sugar and cinnamon in a small bowl. Add melted butter and mix with a fork to form a crumbly topping. Chill while you make the batter.

The butter, gf flour, cinnamon and brown sugar for the crumb topping in small bowls on a grey marble background.

Mix the dry ingredients

Sift the gluten free flour, baking powder, cinnamon and xanthan gum (if using) into a large bowl. Whisk in the brown sugar and break up any lumps.

The sifted and whisked dry ingredients, with the brown sugar added.

Mix the wet ingredients

Warm the milk and butter together (microwave briefly) until the butter is mostly melted. Stir until fully combined, then whisk in the egg, yoghurt and vanilla.

The melted butter and milk in a glass jug.

Prepare the apples

Peel, core and chop the apples into roughly 1cm (1/2″) pieces. Weigh out about 200g of chopped apple.

A peeled red apple on a blue chopping board, next to a bowl of chopped apple.

Combine and fill

Pour the wet ingredients into the dry and stir gently until almost combined, with a few streaks of flour remaining. Fold in the chopped apples so they’re evenly distributed.

The mixed muffin batter with chunks of apple evenly mixed in.

Spoon the batter evenly into the muffin tin (a cookie scoop helps). Sprinkle the crumble topping over each muffin; you may not need all of it.

The crumble topping being sprinkled on top of the muffin batter.

Bake

Bake at 200°C (390°F) for about 20 minutes, or until the tops are lightly golden and a skewer inserted into the center comes out clean. Let the muffins rest briefly in the pan, then transfer to a wire rack to cool.

Gluten free apple muffins in a metal muffin pan, with a red apple and small dish of cinnamon streusel.

Serving idea

These muffins are delicious on their own, and they’re also lovely with a drizzle of caramel. For an indulgent twist try a little rum caramel or salted caramel on top.

A apple muffin drizzled with rum caramel sauce.

Storing the muffins

Best enjoyed warm, leftovers keep in an airtight container at room temperature for 1–2 days. The crumble topping will soften over time. To refresh slightly dried muffins, wrap one in a damp paper towel and microwave for 10–20 seconds.

Freezing

These muffins freeze well, though the crumble can become a little soft. If you plan to freeze, you may prefer to leave the crumble off and add fresh topping after defrosting. Wrap muffins individually or in pairs in plastic wrap, place in an airtight container or freezer bag, and freeze for up to 2 months. Defrost at room temperature or in the microwave.