37 Irresistible Apple Muffins to Cozy Up Your Fall Mornings

Welcome to Apple Muffin Heaven!

There’s something magical about the aroma of apple muffins baking in the oven as the leaves begin to change. Whether you’re a early riser looking for a grab-and-go breakfast or someone who enjoys a sweet treat with afternoon tea, these 37 apple muffins recipes offer something for everyone! From savory options with cheese and herbs to sweet classics with cinnamon and crumb toppings, you’ll find new ways to transform this humble fruit into delicious baked goods.

As someone who’s tested hundreds of muffin recipes, I can tell you that apple muffins are uniquely versatile — they work beautifully with both sweet and savory flavor profiles. The natural moisture from the apples creates an incredibly tender crumb that stays fresh longer than other varieties. Ready to discover your new favorite apple muffin recipe? Let’s dive in!

1. Savory Apple Cheddar Muffins

These savory apple cheddar muffins bring together the perfect balance of sweet Honeycrisp apples and sharp cheddar cheese in every bite. The hint of black pepper and fresh thyme elevates these beyond your typical muffin, making them an excellent companion to soups or salads. They’re hearty enough for breakfast but sophisticated enough to serve alongside dinner.

2. Apple Rosemary Muffins with Sharp Cheddar

The fragrant combination of fresh rosemary and sweet-tart apples creates an aromatic muffin that’s impossible to resist. Each bite delivers pockets of melted sharp cheddar that perfectly complement the herbaceous notes and apple chunks. These sophisticated muffins make a stunning addition to a brunch spread or alongside a bowl of butternut squash soup.

3. Apple Thyme Muffins with Polenta

The delightful textural contrast of cornmeal polenta and tender apple chunks makes these muffins truly special. Fresh thyme infuses the batter with subtle herbal notes that complement the natural sweetness of the apples. These rustic muffins have a beautiful golden crust and stay moist for days, if they last that long!

4. Bacon Apple Cheddar Muffins

These hearty bacon apple cheddar muffins combine three irresistible flavors into one perfect breakfast package. Crispy bacon pieces, sweet-tart apple chunks, and pockets of melted cheddar create a flavor explosion in every bite. Perfect for meal prep, these protein-rich muffins will keep you satisfied all morning long.

5. Apple Sausage Breakfast Muffins

These savory breakfast powerhouses combine sweet apples with savory breakfast sausage for a complete meal in muffin form. Golden brown on the outside and moist inside, they feature a fabulous blend of sage, maple, and apple flavors. Make a batch on Sunday for grab-and-go breakfasts all week long – they reheat beautifully in just 20 seconds!

6. Caramelized Onion and Apple Muffins

Sweet meets savory in these sophisticated muffins featuring slowly caramelized onions and chunks of tart Granny Smith apples. The deep umami flavor of the onions balances perfectly with the bright apple notes, creating an unexpected flavor combination that’s utterly addictive. These elegant muffins pair perfectly with a bowl of tomato soup or alongside a cheese board.

7. Prosciutto and Apple Muffins with Sage

These elegant muffins feature thin slices of prosciutto wrapped around tender chunks of apple, with fresh sage leaves infusing every bite. The salty-sweet combination creates a sophisticated flavor profile that’s perfect for brunch or as an accompaniment to a festive dinner. The prosciutto crisps up beautifully around the edges, adding wonderful textural contrast.

8. Apple and Gouda Muffins with Walnuts

Smoky gouda cheese creates perfect pockets of meltiness in these apple walnut muffins. The buttery walnuts add wonderful crunch and nutty flavor that complements the sweet-tart apple chunks throughout. These hearty muffins make an excellent on-the-go breakfast option or an elegant side for your favorite autumn soup.

9. Jalapeño Cheddar Apple Cornbread Muffins

These kicks-it-up-a-notch muffins combine the sweetness of apple with spicy jalapeños and sharp cheddar in a cornbread base. The genius combination creates a perfect sweet-spicy-savory balance that’s irresistible alongside chili or barbecue. The cornmeal gives these muffins wonderful texture while the apples keep everything moist and tender.

10. Apple Chai Spice Muffins

These fragrant muffins capture all the warming spices of your favorite chai latte—cardamom, cinnamon, ginger, and cloves—paired with sweet chunks of apple. The aromatic spice blend infuses every bite, while a crunchy cardamom sugar topping creates the perfect textural contrast. Perfect with your morning coffee or afternoon tea, these muffins will fill your kitchen with the most heavenly scent.

11. Miso Caramel Apple Muffins

These innovative muffins feature a surprising twist—miso paste is incorporated into the caramel drizzle, adding a complex umami note that elevates the classic caramel apple combination. The sweet-savory balance creates depth of flavor you won’t find in ordinary muffins. Tender apple chunks throughout ensure each bite delivers the perfect amount of fruit.

12. Brown Butter Apple Muffins with Sage

The nutty aroma of brown butter transforms these apple muffins into something truly special. Fresh sage adds an unexpected herbal note that pairs beautifully with the sweet apples and rich nutty butter. These sophisticated muffins strike the perfect balance between sweet and savory, making them versatile enough for breakfast or alongside a hearty autumn dinner.

13. Apple Cardamom Muffins with Pistachio Crumble

Fragrant cardamom and sweet apple create a heavenly combination in these elegant muffins topped with a crunchy pistachio crumble. The bright green pistachios add beautiful color and nutty flavor that complements the apple-cardamom pairing perfectly. These bakery-worthy treats look as stunning as they taste, making them perfect for special brunches or gifting.

14. Ginger Apple Muffins with Lemon Glaze

These zippy muffins feature both fresh and crystallized ginger for a double dose of warm, spicy flavor that pairs perfectly with chunks of sweet apple. The bright lemon glaze adds a refreshing tang that balances the warmth of the ginger beautifully. These vibrant muffins are perfect for waking up your taste buds on sleepy mornings.

15. Bourbon Soaked Apple Pecan Muffins

These grown-up muffins feature apples soaked in bourbon, infusing them with warm caramel notes that perfectly complement the toasted pecans. The rich, complex flavor profile makes these muffins feel indulgent and special. Perfect for holiday brunches or as a sophisticated dessert when topped with a scoop of vanilla ice cream.

16. Maple Tahini Apple Muffins

These innovative muffins combine the nutty richness of tahini with pure maple syrup and sweet-tart apples for a uniquely delicious treat. The tahini adds wonderful moisture and a subtle sesame flavor that pairs surprisingly well with the apples. Topped with a maple tahini drizzle, these muffins offer complex flavors that will have everyone asking for your secret recipe.

17. Earl Grey Infused Apple Muffins

These elegant muffins feature milk steeped with Earl Grey tea, infusing the batter with subtle bergamot notes that complement the sweet apples beautifully. The delicate tea flavor adds sophistication while a light vanilla glaze enhances the fruity notes. Perfect for afternoon tea or a refined breakfast option that pairs wonderfully with your morning cuppa.

18. Apple and Pear Muffins with Crystallized Ginger

These fruit-forward muffins combine the best of fall’s harvest—apples and pears—with spicy bits of crystallized ginger throughout. The two fruits create delightful textural variety while the ginger adds warmth and zing to each bite. These moist, flavorful muffins stay fresh for days and make a perfect seasonal breakfast or afternoon snack.

19. Sourdough Apple Cinnamon Muffins

These ingenious muffins put your sourdough discard to delicious use, creating tender apple muffins with complex flavor and wonderful texture. The natural tanginess of the sourdough perfectly balances the sweet apples and warming cinnamon. These hearty muffins are more nutritious than standard versions thanks to the fermentation process of the sourdough.

20. Air Fryer Apple Fritter Muffins

Get the taste of apple fritters without the mess of deep frying! These genius air fryer muffins deliver crispy, caramelized exteriors and tender, apple-studded interiors, finished with a sweet glaze just like classic fritters. Ready in less than 15 minutes and much healthier than traditional fried versions, these muffins will quickly become a family favorite.

21. Cream Cheese Stuffed Apple Muffins

These delightful muffins hide a sweet surprise—a pocket of tangy cream cheese filling nestled in a tender apple-cinnamon batter. The contrast between the creamy filling and the apple-studded muffin creates a cheesecake-like experience in portable form. Perfect for special brunches or when you need a little treat to brighten your day.

22. Apple Butter Swirl Muffins

These gorgeous muffins feature beautiful swirls of spiced apple butter throughout a tender vanilla batter studded with fresh apple chunks. The concentrated flavor of the apple butter adds incredible depth while creating stunning patterns in each muffin. The double dose of apple—both fresh and in butter form—makes these muffins incredibly moist and flavorful.

23. Bakery Style Jumbo Apple Crumb Muffins

These impressive oversized muffins rival anything you’d find in a professional bakery, with their generous apple chunks and thick brown sugar-cinnamon crumb topping. The muffin tops spread beautifully, creating the perfect canvas for the abundant buttery crumble. These showstoppers are perfect for special breakfasts when you want to impress without spending hours in the kitchen.

24. Mini Apple Muffins with Cinnamon Sugar

These adorable bite-sized muffins are rolled in cinnamon sugar while still warm, creating a delightfully crunchy exterior similar to a donut hole. The tender apple-studded interior provides the perfect contrast to the sweet, spiced coating. Their small size makes them perfect for little hands, lunch boxes, or when you just want a tiny sweet treat without overindulging.

25. Upside-Down Caramel Apple Muffins

These stunning muffins feature caramelized apple slices on the bottom that become the beautiful top when inverted after baking. The buttery caramel sauce creates a gorgeous glaze over the perfectly arranged apple slices, while the tender muffin beneath soaks up all those wonderful flavors. These impressive treats taste like individual apple upside-down cakes in convenient muffin form.

26. Gluten-Free Apple Cinnamon Muffins

These tender gluten-free muffins prove that dietary restrictions don’t mean sacrificing flavor or texture. A carefully tested blend of alternative flours creates a perfectly moist muffin studded with cinnamon-spiced apple chunks. Even those without gluten sensitivities will reach for seconds of these delicious, tender muffins that stay fresh for days.

27. Vegan Apple Cider Oat Muffins

These plant-based muffins get incredible flavor from concentrated apple cider and hearty texture from rolled oats. Completely dairy-free and egg-free, they still achieve a tender crumb and perfect moisture thanks to clever ingredient substitutions. The robust apple flavor comes through beautifully, making these a fall favorite for vegans and non-vegans alike.

28. Paleo Apple Walnut Muffins

These grain-free muffins combine almond and coconut flours with fresh apples and crunchy walnuts for a nutritious paleo-friendly treat. Sweetened with just maple syrup and the natural sugars from the apples, these muffins provide sustained energy without the crash. Perfect for those following paleo, primal, or clean eating lifestyles.

29. Keto Apple Spice Muffins

These clever low-carb muffins recreate the flavor of apple muffins without the carbs by using a secret ingredient—zucchini—flavored with apple extract and warm spices. The texture and taste will satisfy your apple muffin cravings while keeping you in ketosis. With less than 4g net carbs per muffin, they’re a guilt-free way to enjoy fall flavors on a ketogenic diet.

30. High Protein Apple Greek Yogurt Muffins

These powerhouse muffins pack over 8g of protein each, thanks to Greek yogurt and a touch of protein powder in the batter. The yogurt creates an incredibly moist texture while diced apples add natural sweetness and fiber. These satisfying muffins make a perfect post-workout snack or busy morning breakfast that will keep hunger at bay for hours.

31. Sugar-Free Apple Muffins

These perfectly sweet muffins contain no added sugar, relying instead on the natural sweetness of apples and a touch of monk fruit sweetener for balance. Perfect for diabetics or anyone monitoring their sugar intake, these muffins don’t compromise on flavor or texture. The apple chunks and warm spices create a satisfying treat that won’t spike your blood sugar.

32. Whole Wheat Apple Carrot Muffins

These nutritious muffins sneak in both apples and carrots for a double dose of produce in every bite. Made with 100% whole wheat flour, they’re hearty and satisfying while remaining light and moist thanks to the fruit and vegetables. These kid-friendly muffins make perfect lunchbox additions or after-school snacks that you’ll feel good about serving.

33. Flourless Apple Oatmeal Muffins

These innovative muffins use blended oats instead of flour for a nutritious, whole-grain treat that’s naturally gluten-free. Packed with diced apples, warming spices, and a touch of maple syrup, they offer the comforting flavors of apple oatmeal in convenient muffin form. Perfect for busy mornings or as a wholesome afternoon snack with a cup of tea.

34. Vegan Apple Rosemary Olive Oil Muffins

These sophisticated vegan muffins use high-quality olive oil for richness and fresh rosemary for an unexpected herbal note that pairs beautifully with sweet-tart apples. The combination creates a uniquely savory-sweet muffin that’s perfect for those who prefer treats that aren’t too sweet. These elegant muffins make a wonderful accompaniment to a hot cup of coffee or tea.

35. Gluten-Free Apple Thyme Savory Muffins

These savory gluten-free muffins feature fresh thyme, Granny Smith apples, and a blend of alternative flours for perfect texture without wheat. The combination of herbaceous thyme and tart apples creates a sophisticated flavor profile that’s perfect alongside soups, stews, or salads. These versatile muffins make gluten-free dining feel luxurious rather than restrictive.

36. Low-Calorie Apple Bran Muffins

These fiber-rich muffins pack major nutrition with minimal calories—just 145 per muffin. Wheat bran and diced apples provide filling fiber while applesauce replaces oil to keep the calories in check without sacrificing moisture. Perfect for weight management or anyone looking for a nutritious breakfast option that will keep you satisfied through the morning.

37. Keto Apple Cheddar Muffins

These clever keto-friendly muffins use jicama as a low-carb substitute for apple, seasoned with apple pie spice to create the perfect flavor illusion. Sharp cheddar adds savory notes and helps create a tender crumb without the need for traditional flour. With just 3g net carbs per muffin, they’re a perfect option for those following ketogenic or low-carb lifestyles.

Apple Muffin Goodness Year-Round!

From savory delights packed with cheese and herbs to sweet classics with cinnamon and crumble, these 37 apple muffin recipes prove just how versatile this beloved fruit can be. Whether you’re looking for a quick breakfast, a nutritious snack, or a comforting treat, there’s an apple muffin recipe here to satisfy your craving.

What makes apple muffins so special is their ability to stay moist and delicious for days after baking, thanks to the natural moisture in the apples. They’re perfect for meal prep, lunch boxes, or unexpected guests. Plus, with so many dietary variations included—from keto to vegan to gluten-free—everyone can enjoy these wonderful treats regardless of their nutritional needs.

I’d love to know which apple muffin recipe you’ll try first! Leave a comment below sharing your favorite or bookmark this page so you can work your way through the collection. For more seasonal recipes featuring fall’s bounty, check out our pumpkin bread collection or sign up for our newsletter to get fresh baking inspiration delivered straight to your inbox.

Happy baking!

Frequently Asked Questions

What’s the best apple variety for apple muffins?

Firm, tart-sweet apples generally work best in muffins as they hold their shape during baking and provide good flavor contrast. Honeycrisp, Pink Lady, Braeburn, and Granny Smith are excellent choices. For savory muffins, Granny Smith’s tartness works particularly well, while sweeter varieties like Honeycrisp or Gala are perfect for dessert-style muffins.

Can I freeze apple muffins?

Absolutely! Most apple muffins freeze beautifully for up to 3 months. Allow them to cool completely, then wrap individually in plastic wrap and place in a freezer bag. Thaw at room temperature or microwave for 20-30 seconds when ready to enjoy. Muffins with streusel toppings may lose some crunchiness when frozen, but will still taste delicious.

How do I keep apple muffins moist?

The apples themselves add significant moisture, but some additional tips include: not overmixing the batter, using oil instead of butter, adding yogurt or applesauce, and storing in an airtight container with a piece of paper towel to absorb excess moisture. Also, avoid overbaking – remove muffins when a toothpick inserted comes out with a few moist crumbs.

Can I make these muffin recipes into a loaf?

Most muffin recipes can be converted to a loaf, though baking time will increase significantly (typically 45-60 minutes instead of 18-22 for muffins). Use a 9×5-inch loaf pan and reduce the oven temperature by 25°F to prevent over-browning. Check for doneness with a toothpick inserted in the center – it should come out clean or with a few moist crumbs.