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Best Healthy Fall Dessert Recipes with Pumpkin and Cozy Flavors

When the air turns crisp and leaves start to fall, there's nothing quite like baking up a batch of your favorite cozy treats.

This roundup of the best healthy fall dessert recipes is all about indulgence—without the guilt. With naturally sweetened ingredients, warm spices, and seasonal favorites like pumpkin, apple, and pecan, you'll find everything you need for your fall baking adventures.

These dessert recipes are gluten-free, low-carb, and made with healthier ingredients, so you can enjoy them whether you're looking for a healthy fall dessert, an easy fall baking idea, or a macro-friendly treat to fit into your goals.

What makes a fall dessert healthy

Healthy fall desserts are all about rich flavors paired with smart swaps. Instead of processed sugar and refined flours, opt for naturally sweetened options, such as alternative sweeteners or sweetened maple syrup (or sugar-free syrup), and use almond flour, coconut flour, and pumpkin puree. These healthier recipes are still decadent, just made with ingredients that are better for your body.

Keep a jar of this mix on hand and you’ll be ready to elevate all your fall baking—from pumpkin muffins to pecan pie.

Creamy and delicious healthy pumpkin pie

Our Healthy Pumpkin Pie is everything you love about the classic holiday favorite, but better for you. Made with canned pumpkin and sweetened with a sugar-free condensed milk, this dessert is a must-have for any fall table.

It’s the perfect healthy fall dessert—flavorful, smooth, and spiced just right with pumpkin spice. This version is also gluten-free and can be topped with whipped cream or a drizzle of caramel sauce for that extra special touch.

Soft pumpkin chocolate chip muffins

These Pumpkin Chocolate Chip Muffins are packed with fall flavor and just the right amount of sweetness from dark chocolate chips. With a moist texture and warm spices, they make a perfect healthy fall breakfast or dessert.

Made with a low carb flour blend, pumpkin puree, and naturally sweetened ingredients, these muffins are gluten-free and totally crave-worthy. Pair one with a pumpkin spice chai or latte for a cozy fall treat.

Fudgy low-carb pumpkin brownies

Our Keto Pumpkin Brownies are a rich, chocolate pumpkin dessert that combines everything you love about brownies with the seasonal goodness of pumpkin. They're dense, chocolatey, and full of pumpkin spice.

These gluten-free brownies are perfect when you're craving something decadent but want to stick to your healthy eating goals. Naturally sweetened, made with almond flour and dark chocolate chips, they’re one of the best healthy fall baking options for chocolate lovers.

Cozy pumpkin mug cake in minutes

The Pumpkin Chocolate Chip Muffin in a Mug is a quick and easy way to enjoy dessert without the wait. With just a few ingredients—like canned pumpkin, almond flour, and chocolate chips—you can whip up a warm, gooey mug cake in under five minutes.

This pumpkin mug cake is naturally sweetened, macro-friendly, and totally satisfying when your sweet tooth hits. Top it with a dollop of the cream cheese frosting or almond butter for an extra layer of flavor.

Naturally sweetened pumpkin spice cupcakes

Our Pumpkin Spice Cupcakes are perfectly spiced and topped with a maple cream cheese frosting that’s naturally sweetened. These cupcakes are light, fluffy, and full of fall flavor.

With ingredients like pumpkin puree, almond flour, and pumpkin spice, these cupcakes are one of the best healthy fall desserts to bring to gatherings or enjoy at home. The cream cheese frosting is just sweet enough and makes them feel extra special.

Sweet and creamy pumpkin pie fudge

This Pumpkin Pie Fudge is a quick, no-bake treat that tastes like a bite of creamy pumpkin pie in candy form. It's naturally sweetened and has a rich, melt-in-your-mouth texture that makes it irresistible.

Made with canned pumpkin and warm spices, this fudge is a unique addition to your lineup of pumpkin desserts. It’s a great dessert option to prep ahead or package as a gift during the fall season.

Pumpkin pecan chocolate chip protein bars

These Pumpkin Protein Bars are the perfect balance of sweet and satisfying. Made with pumpkin puree, chopped pecans, and chocolate chips, they’re soft, chewy, and packed with protein to keep you full for longer.

These healthy pumpkin bars are ideal for meal prep or a post-workout snack. They're macro-friendly, gluten-free, and naturally sweetened—great for keeping on hand all season long.

Cinnamon cream cheese frosted pumpkin bars

The Pumpkin Bars with Cinnamon Cream Cheese Frosting are an easy fall dessert recipe that checks all the boxes. Soft, spiced pumpkin cake with a rich cream cheese frosting makes this a fan favorite.

Naturally sweetened and gluten-free, these bars are perfect for entertaining or as a treat for yourself. The combination of pumpkin and cream cheese makes them taste like a bakery-style indulgence—without all the added sugar.

Warm cinnamon spice cake with cream cheese frosting

This Cinnamon Spice Cake is the kind of cozy, classic dessert that belongs in every fall baking lineup. Flavored with warm spices and topped with a silky cream cheese frosting, it's a healthier version of a traditional spice cake that still delivers all the indulgence.

Made with wholesome, gluten-free ingredients like almond flour and naturally sweetened with your favorite low-carb sweetener, this cake is ideal for gatherings, potlucks, or simply enjoying with a cup of tea.

Caramel apple desserts that are gluten-free

For the apple lovers, our Low-Carb Caramel Apple Fries are a fun twist on a classic caramel apple. Spoiler alert - it's not actually apple, but try it with a drizzle of Maple Salted Caramel Sauce, and I'm sure you'll love it!

Frosted pumpkin snickerdoodles with cream cheese filling

The Pumpkin Snickerdoodles with Cream Cheese Filling are soft, chewy, and loaded with fall flavor. With a cinnamon-sugar coating and creamy filling, they’re a standout in the world of pumpkin desserts.

They’re naturally sweetened, gluten-free, and made with real pumpkin puree. Whether you’re baking for a party or just treating yourself, these little pumpkin cookies are sure to be a hit.

Classic sugar-free pecan pie made healthy

This Sugar-Free Pecan Pie is a must-have for your fall dessert table. With a rich, gooey filling and crisp pecan topping, it delivers everything you love about traditional pecan pie—without the sugar or guilt.

Made with healthier ingredients and a buttery almond flour crust, this gluten-free version is naturally sweetened and perfect for holiday gatherings. Whether served warm with a dollop of whipped cream or chilled from the fridge, it’s one of the best healthy fall dessert recipes to impress your guests.

Easy low-carb pecan pie bars with oat-inspired flavor

These Low-Carb Pecan Pie Bars are a delicious twist on the classic pie—perfectly portioned for parties, lunchboxes, or a quick fall dessert at home. The layers of almond flour crust and crunchy pecan topping make them irresistibly satisfying.

Naturally sweetened and gluten-free, these bars have the comforting taste of a pecan pie with the ease of a grab-and-go treat. If you're a fan of nutty fall desserts, this one checks every box and brings all the decadence of pecans without the added sugar.

Cozy apple pie oatmeal pancakes for a healthy fall breakfast

These Apple Pie Pancakes are made with oat flour, bringing all the warm, nostalgic flavors of a classic apple pie into a light, fluffy, and totally guilt-free breakfast. With tender bites of cinnamon apple in every stack, they’re perfect for chilly mornings and lazy weekend brunches.

This is the only recipe in this post that isn't low-carb, but it is made with wholesome ingredients. These pancakes are low-fat, sugar-free, and gluten-free—making them a great choice for a healthy fall treat that still satisfies your sweet tooth. They offer a cozy blend of apple pie flavor and fall dessert vibes, but in a format that’s nourishing and energizing. Top them with a drizzle of pure maple syrup or a dollop of Greek yogurt for the perfect finish.

Favorite fall drinks for dessert lovers

Round out your dessert table with a warm Pumpkin Spice Latte or a cozy Pumpkin Spice Chai. These fall drinks are naturally sweetened and full of comforting spices.

They’re perfect served with muffins, cookies, or as a dessert on their own. Add a swirl of cream, sprinkle some pumpkin spice on top, and sip your way into the season.