9 Healthy Muffin Recipes Way Better Than the Store-Bought Versions (2024)

Healthy muffin recipes do exist! Contrary to the nutrition info on the jumbo ones you find at convenience stores or order at a bakery, these made-from-scratch healthy breakfast muffins offer well-balanced nutrition and yummy flavor. With summery healthy blueberry muffins and healthy banana muffins plus fitting-for-fall healthy pumpkin muffins and healthy apple muffins, each of these options has fewer than 200 calories per serving.

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Apple-Streusel Muffins

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Spice up your morning routine with a warm and crumbly apple and streusel muffin. Laced with brown sugar and packed with flaxseeds, pecans, and sliced apples, these healthy apple muffins are perfect as part of a seasonal fall breakfast menu. With four grams of protein, each makes a solid, well-balanced mini meal when served with a carton of Greek yogurt.

Healthy muffin calories: 163

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Customizable Healthy Muffins

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This healthy muffin recipe is a blank canvas for all kinds of fun flavors, including lemon-poppy seed, blueberry, cheese, and oatmeal variations. (For more fiber, use half each of all-purpose and whole wheat flour as the base.) Choose your favorite, then get to mixing. All told, you're investing just 10 minutes of prep time. Before baking, top 'em all off with our sweet and simple streusel topping.

Healthy muffin calories: 136

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Blueberry and Oat-Chia Seed Muffins

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Each 1-ounce serving of chia seeds packs in about a whopping five grams of plant-based protein. Those superfood seeds star along with one of the most antioxidant-rich fruits in this healthy blueberry muffin recipe. A mix of oats and flour in the dry ingredient mixture makes these taste far more hearty than you might imagine for mini muffins.

Healthy muffin calories: 108

Savory Spaghetti Squash Muffins

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9 Healthy Muffin Recipes Way Better Than the Store-Bought Versions (4)

If you're firmly on Team Savory, this roundup is still for you! Featuring spaghetti squash, fresh chives, garlic powder, and Monterey Jack cheese with jalapeño peppers, this muffin under 150 calories makes one delightful (and fairly low-carb) dinner side. Try it as an addition to the meal next time you make grilled chicken, steak, or a pasta entrée.

Healthy muffin calories: 134

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Curried Squash Muffins

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Warmly spiced and reminiscent of some of our favorite flavors from Indian cuisine, this is one of the most interesting and easy healthy muffin recipes ever developed in our Test Kitchen. Curry powder and roasted butternut squash pair up in the batter that clocks in at fewer than 150 calories per muffin. Dust the tops with powdered sugar for a sweet and showy finish.

Healthy muffin calories: 141

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Ginger-Blueberry Muffins

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Worried that lightened-up muffins might be dense and dry? This recipe is about to convince you otherwise. Cake flour ($5, Target) gives these updated healthy blueberry muffins their fluffy texture. Thanks to molasses, fresh ginger, and other cozy spices, this might just become your go-to blueberry muffin recipe.

Healthy muffin calories: 167

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Peach-Prosciutto Cornmeal Muffins

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Perhaps you've sprinkled your corn bread with bacon before. But have you tried stirring bacon's delicious cousin, prosciutto, into bread recipes? A little bit goes a long way to add a hint of salty-savory goodness and some muscle-building power to these healthy protein muffins. (Each muffin has as much protein as an egg!) Don't fret if it's not fresh peach season; frozen peaches work wonderfully to balance out that savory element with some natural sweetness.

Healthy muffin calories: 184

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Gluten-Free Zucchini Muffins with Greek Yogurt Frosting

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Take a break from the oodles of zoodles and put your zucchini haul to good use in these healthy applesauce muffins. A cup of the shredded squash teams up with a half cup of unsweetened applesauce to make the crumb of these you'd-never-guess-they're-gluten-free muffins remarkably tender and moist. Crown with a layer of vanilla-scented Greek yogurt frosting and you might just think you're devouring a cupcake.

Healthy muffin calories: 164

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Wheat Bran Muffins

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9 Healthy Muffin Recipes Way Better Than the Store-Bought Versions (9)

Since we don't have time every day to whip up a healthy breakfast muffin recipe from scratch, we love stocking a batch or two of the batter for these muffins in our freezer. If you, too, want to get a jump-start, mix up the wheat bran and buttermilk mixture entirely in advance, freeze for up to a month, then thaw, portion into muffin tin cups, and bake for a warm, fresh-baked batch. For a variety of flavors, portion out one cup of batter into three bowls, then dress one up with chopped dates and apples, another with shredded carrots and golden raisins, and the last with semisweet chocolate pieces and chopped toasted pecans.

Healthy muffin calories: 196