Recipes > Breakfast > Healthy Apple Cinnamon Muffins with Walnuts

Healthy Apple Cinnamon Muffins with Walnuts

We doubt you’ll be able to resist biting into a warm, fluffy muffin when it’s fresh out of the oven! Enjoy on its own for a satisfying snack or dessert, topped with almond butter for a balanced breakfast, or as a sweet addition to lunch.
healthy apple cinnamon muffins on a blue plate with whole apples in the background

This is a variation of our whole wheat muffins base recipe. Is there anything better than a warm, spicy, and fluffy muffin? We don’t think so! These healthy apple cinnamon muffins are packed with fresh apples, whole wheat flour, walnuts, and warming cinnamon – a classic autumn combo guaranteed to satisfy the senses!

Three Must Know Cooking Skills

For recipe success, learn how to:

Culinary Tips for the Best Healthy Apple Cinnamon Muffins

Measure the flour properly to prevent dense muffins. Fluff, spoon, and level; don’t scoop and pack! 

Whisking the dry ingredients together mimics sifting and evenly distributes the ingredients, so don’t substitute another utensil.

Toast the walnuts for best flavor. Place on a baking sheet and bake at 350ºF for 5-10 minutes or until they smell toasty. Allow to cool slightly, then add to the dry ingredients after whisking to ensure even distribution.

Don’t overmix the batter! Watch our muffin method culinary technique video to learn how to mix the batter just enough so that you end up with light and fluffy muffins.

When measuring brown sugar, pack it in the cup. If you are trying to reduce your sugar consumption or prefer less sweet muffins, reduce the sugar to ⅓ cup; the recipe will still come out great!

We use a dark non-stick muffin pan to bake these muffins. If you use a light colored pan, the cooking time will increase. To check for doneness, insert a toothpick into a muffin in the middle of the pan. If it comes out clean, it’s done! 

Use a portion scoop to distribute the batter into the muffin tins. This handy tool can help make perfect muffins, cupcakes, pancakes, and more. It also makes the work easier; just squeeze the handle, and the batter slides right out!

Ingredient Substitutions

  • White Whole Wheat Flour: substitute whole wheat pastry flour or spelt flour for a similar taste, color, and texture. You can also substitute 1 cup whole wheat flour and ½ cup all-purpose flour. To make gluten-free apple cinnamon muffins, use a gluten-free flour mix, such as Bob’s Red Mill 1-to-1 Gluten-Free Flour.
  • Cinnamon: substitute pumpkin pie spice or apple pie spice. You can also substitute ¼ teaspoon cinnamon with ginger, cardamom, cloves, nutmeg, allspice, or a combination.
  • Kosher Salt: We use Morton kosher salt. If using Diamond Crystal kosher salt, use ¾  teaspoon. If you use table salt, use slightly less than ½ teaspoon. 
  • Walnuts: substitute raw or toasted chopped almonds, pecans, sunflower seeds, pumpkin seeds, hemp seeds, or flax seeds. 
  • Apples: substitute ½ cup of the shredded apples with shredded zucchini, shredded carrots, mashed ripe bananas, canned pumpkin, pureed butternut squash, or ¼ cup unsweetened applesauce.
  • Buttermilk: substitute plain yogurt, Greek yogurt, kefir, or sour cream. You can also make your own buttermilk by mixing ½ cup milk or milk alternative with ½ Tablespoon white vinegar or lemon juice.
  • Brown Sugar: substitute cane sugar, turbinado sugar, or coconut sugar, but note that the flavor will be slightly different. 
  • Canola Oil: substitute avocado oil. Do not substitute olive oil, as this has a strong flavor. Do not substitute vegetable oil, as this is not a heart-healthy oil.
  • Eggs: to make vegan apple cinnamon muffins, substitute the eggs with flax eggs. To make two flax eggs, mix 2 Tablespoon ground flaxseeds with 6 Tablespoons water and let rest for 10 minutes. Eggs help leaven the muffins, so a vegan version might not be quite as fluffy.

Recipe Variations

Want to make mini healthy cinnamon apple muffins? Prepare a mini muffin pan with liners or non-stick spray and bake for 10-12 minutes, or until a toothpick inserted comes out clean.

This healthy apple cinnamon muffin batter works for quick bread too! To make whole wheat apple bread, prepare a 9×5 loaf pan with parchment paper or non-stick spray. Cook for 50-55 minutes, or until a toothpick inserted into the middle comes out clean. 

Want more whole wheat muffin recipe inspiration?

Use our base recipe as a guide, or try out these tasty variations!

Equipment Recommendations

Use these kitchen tools for recipe success:

Find all of our favorite kitchen tools here!

Are these easy apple muffins healthy?

These ones are! Many pre-made muffins or store bought mixes contain way too much added sugar. Some even contain up to or even more than your daily allowance of sugar – yikes! The key ingredients that make this muffin recipe healthier than store bought varieties are whole wheat flour, apples, walnuts, and less sugar than leading brands.

Whole Wheat Flour

Whole wheat flour is a good source of fiber, B vitamins, Vitamin E, trace minerals, and phytonutrients. Replacing refined grains (i.e. white flour) with whole grains (i.e. whole wheat flour) may reduce the risk of developing chronic conditions such as heart disease, diabetes, and certain types of cancer.


Does an apple a day keep the doctor away? It certainly can help! Apples contain prebiotic fibers which support gut health. Apples also contain phytonutrients such as quercetin and catechin which may play roles in cancer and cardiovascular disease prevention. For best nutrition, leave the peel on.


Walnuts contain plant-based protein and healthy fats. These nutrients help you feel satisfied until your next meal. Walnuts contain plant-based omega-3 fatty acids that promote brain and heart health.

Less Added Sugar

High sugar consumption is not good for health, and in general, most Americans eat way too much. Men should aim to consume less than 9 teaspoons (~36 grams) of sugar per day, and women should aim to consume less than 6 teaspoons (~24 grams) of sugar per day. Each muffin in this recipe has ~2 teaspoons (8 grams) of added sugar. 

Learn more about health benefits of different foods and ingredients in our book, To Your Taste!

Serving Suggestions for Whole Wheat Apple Muffins

We doubt you’ll be able to resist biting into a warm, fluffy muffin when it’s fresh out of the oven! Enjoy on its own for a satisfying snack or dessert, topped with almond butter for a balanced breakfast, or as a sweet addition to lunch.

Storage Tips for Homemade Healthy Apple Muffins

Because these are moist apple cinnamon muffins, they will spoil more quickly at room temperature. Cool completely, then store in a bag or airtight container at room temperature for a few days or in the refrigerator for up to one week.

Got a busy few weeks ahead? These muffins are great for the freezer! Cool completely, wrap individually or in pairs, then store in a freezer-safe bag for up to 3 months. When ready to eat, thaw overnight in the refrigerator, or reheat in the microwave in the morning

Want more healthy whole grain recipes?

Try out these favorites, and as always, adjust to YOUR taste!

Whole Grain Pancakes Base Recipe

Overnight Oats Base Recipe

Baked Oatmeal Cups Base Recipe

Whole Wheat Quick Bread Base Recipe

Stovetop Oatmeal Base Recipe

healthy apple cinnamon muffins on a blue plate with whole apples in the background

Healthy Apple Cinnamon Muffins with Walnuts

This is a variation of our whole wheat muffins base recipe. Is there anything better than a warm, spicy, and fluffy muffin? We don’t think so! This whole wheat muffins base recipe teaches you the correct ratios of ingredients, then allows you to adjust the ingredients to YOUR taste!
Prep Time 10 minutes
Cook Time 20 minutes
Total Time 30 minutes
Course Breakfast, Snack
Cuisine American
Servings 12 muffins


  • 1 ½ cups white whole wheat flour*
  • 2 teaspoons cinnamon
  • 1 teaspoon baking soda
  • 1 teaspoon baking powder
  • ½ teaspoon kosher salt
  • ½ cup toasted, chopped walnuts
  • 1 large or 2 small apples, shredded (~1 cup)
  • ½ cup buttermilk
  • ½ cup packed brown sugar
  • ¼ cup canola oil
  • 2 large eggs
  • 1 teaspoon vanilla extract


  • Preheat oven to 350°F. Prepare a 12-cup muffin pan with non-stick spray or muffin liners.
  • In a large bowl, gently whisk flour, cinnamon, baking soda, baking powder, and salt. Add walnuts to flour mixture. Toss to evenly coat.
  • In a separate medium bowl, whisk together shredded apple, buttermilk, brown sugar, oil, eggs, and vanilla.
  • Add buttermilk mixture to flour mixture. Using a spatula, fold ingredients just until moistened. Do not overmix.
  • Use a ¼ cup portion scoop to divide out the batter. Cook for 18-20 minutes, or until a toothpick inserted comes out clean. Enjoy!


*substitute 1 cup whole wheat flour + ½ cup all purpose flour or 1 ½ cups whole wheat pastry flour.
Keyword Healthy Apple Cinnamon Muffins

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