Healthy Apple Muffins (Gluten Free)

These Healthy Apple Muffins are moist, tender and full of flavor, thanks to fresh, fiber-rich apples, caramel flavored coconut sugar, and fruity olive oil. Each bite delivers cozy fall comfort with healthy ingredients that make you feel good. Perfect for breakfast, an afternoon pick-me-up, or a satisfying snack on the go.

A muffin in the morning brings simple joy, especially when it’s made with wholesome ingredients that nourish your body. There’s the sensory pleasure of a moist, tender interior, a lightly crisp top, and the ease of a portable, mindful treat. It’s comforting, energizing, and a tender self-care ritual that sets a positive tone for your day.

This is a healthy muffin full of chunks of fresh apple in every bite. The shredded apple makes the muffin moist and tender. Since it’s made with almond flour and sweetened with coconut sugar, it does not spike your blood sugar. You’ll feel calm and balanced.

Olive oil adds a subtle, fruity flavor that complements the fruit and provides a moist, tender texture that keeps muffins soft and fresh longer than butter.  It contains heart-healthy monounsaturated fats and antioxidant properties.

Why You’ll Love These Healthy Apple Muffins

• Moist & Tender – Each bite is soft, fluffy, and filled with juicy bits of fresh apple.
• Naturally Sweetened – Made with coconut sugar for gentle unrefined sweetness.
• Nutrient-Rich Ingredients – Almond flour and olive oil add protein, healthy fats, and a rich, satisfying flavor.
• High in Fiber – Fresh apples and almond flour support digestion and keep you feeling full longer.
• Dairy-Free, Gluten-Free, Grain Free and Paleo – A healthy upgrade that tastes amazing.
• Warm, Cozy Flavor – Cinnamon and apples create the ultimate fall aroma and taste.
• Easy to Make – Simple ingredients, one bowl, no mixer and ready in 30 minutes.
• Freezer-Friendly – Bake once, enjoy all week for quick breakfasts or on-the-go snacks.
• Versatile – Delicious plain or topped with butter, nut butter, ghee, or jam.
• Feel-Good Treat – Wholesome nourishment that satisfies your sweet tooth and uplifts your mood.

Ingredients for Healthy Apple Muffins

These delicious apple muffins are packed with nutritious ingredients but still have that wonderful, cozy muffin flavor and soft tender texture. Here’s what you’ll need to make them:

• Apples:  We use shredded apples to infuse the batter with apple flavor and apple chunks for a more interesting texture (see below for best types of apples).
• Coconut Sugar: Gives the muffins a rich caramel flavor that is has just the right amount of sweetness. You can make these muffins lower in carbohydrate by replacing the coconut sugar with your favorite zero-sugar sweetener.
• Olive Oil: Using olive oil in muffins gives them a rich fruity flavor and makes them soft and moist. They stay longer than muffins made with butter. Also rich in antioxidants. I use it in my Olive Oil Zucchini Bread.
• Eggs: Used to make the muffins fluffy and keep them held together nicely.
• Almond Flour, Tapioca Flour, and Coconut Flour: I use this combination to create the perfect texture without using gluten free flour or white flour. You need all three.
• Almond Milk: Adds moisture, tenderness, and a subtle nutty flavor, and prevents the muffins from becoming dry and crumbly. Any nut milk, coconut milk or diary milk can be substituted.
• Vanilla Extract: A little vanilla enhances the flavor of these healthy apple muffins.
• Cinnamon: This spice provides a warm, sweet, comforting flavor and has a beneficial effect on blood sugar.
• Baking Soda: A natural leavening agent that helps the batter to rise.
• Lemon Juice: The acid reacts with the baking soda, to produce carbon dioxide gas, causing the muffins to rise and become light and fluffy. 
• Sea Salt: Salt brings out all of the flavors in the muffins.
• Walnuts: Just a few to give the topping a little crunch. It’s optional. Pecans are also good.

Best Apples to Use

For muffins, the best apples are firm varieties that will hold their shape when baked, rather than turning to mush. I like a mix of sweet and tart apples for a more complex flavor. Leave the peel on if they’re organic. I usually peel the one I’m grating to make it easier.

Tart firm varieties are Granny Smith, Braeburn or Pink Lady. Firm sweet varieties are Honey Crips and Fuji. A combination is always good when making Apple Crisp

How To Make

This recipe comes together in just 10 minutes using a few bowls, a whisk, and a muffin pan. You’ll need a simple box grater for the apples. If you don’t have one, it’s a wonderful kitchen tool to have on hand, you’ll use often.

I top the muffins with a sprinkle of coconut sugar and walnuts for additional texture but it is optional.

Start by preheating the oven to 375°F and line a muffin tin with muffin cups.

Mix the dry ingredients. Add the flours, baking soda, cinnamon, and salt to a mixing bowl and stir until combined.

Mix the wet ingredients. In a separate bowl, whisk together the eggs, almond milk, coconut sugar, olive oil, vanilla, and lemon juice.

Prepare the apples. Grate the apples and measure. Put into a clean kitchen towel and squeeze out most of the moisture. Chop the remaining apples, measure. Add chopped and grated apples to the dry ingredients.

Mix together. Mix grated and chopped apples with the dry ingredients until they are covered with flour. Pour the wet ingredients into the dry and mix until just combined and no flour is visible.

Fill the muffin cups and bake. Divide the batter evenly between the 12 muffin cups. Sprinkle the tops of the muffins with coconut sugar and chopped walnuts, if using.

Serving

• Serve alone, great for an on-the-go breakfast or snack.
• Heat up and serve with a little butter or ghee.
• Spread with almond butter for extra protein.
• Jam and honey are also delicious.

Storing

• To store: Store at room temperature for 2 to 3 days. After that, store them in the fridge for about one week in an airtight container.
• To freeze: Place them in a freezer-safe container for up to 3 months.
• To reheat frozen muffins: Let thaw at room temperature for 30 minutes before reheating in an air fryer or toaster oven at 350° for 3-5 minutes. If you’re in a hurry wrap them in foil and heat at 300° for 10 minutes, remove foil for the last 2 minutes. For the microwave, heat frozen muffins for 15 seconds per muffin to thaw and warm it through.

These Healthy Apple Muffins are more than just a treat — they’re a nourishing way to start your day or satisfy an afternoon craving. Packed with fiber, protein, and healthy fats from almond flour olive oil and fresh apples, they keep you feeling full, balanced, and energized.

For the best results, use crisp apples like Honeycrisp or Fuji and plenty of cinnamon to enhance the flavor and aroma. Let the muffins cool completely before storing to maintain their perfect texture. Simple to make, naturally sweet, and wonderfully moist, these muffins turn healthy eating into a moment of pure pleasure.

More Delicious Healthy Gluten Free Muffins You Will Love

• Cranberry Orange Muffins – Bright and colorful packed with fresh cranberries, orange juice, orange zest, and almond flour but totally diary free. Enjoy them for breakfast or snack.
• Paleo Pumpkin Muffins – They’re so good you may think you’re eating cake but they’re chock full of protein, fat, and fiber. 
• Pistachio Muffins – A health way to start your day. They’re nutty and tender with a sweet pistachio flavor. 

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