Recipes > Breakfast > Whole Wheat Muffins Base Recipe

Whole Wheat Muffins Base Recipe

This whole wheat muffins base recipe teaches you the correct ratios of ingredients, then allows you to adjust the ingredients to YOUR taste!
three whole wheat muffins on a plate with a pan of muffins in the background

This is one of our base recipes. 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! Packed with fresh and dried fruits and/or veggies, whole grains, nuts, and a touch of spice, this basic muffin recipe is going to quickly become a staple in your house!

Three Must Know Cooking Skills

For recipe success, learn how to:

Culinary Tips for the Best Homemade Muffin Recipe

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.

Add the dried fruit, nuts, seeds, or chocolate chips after whisking the dry ingredients to ensure even distribution.

Add shredded or pureed fruits or vegetables with the liquid ingredients.

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!

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!

To check for doneness, insert a toothpick into a muffin in the middle of the pan. If it comes out clean, it’s done! 

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. Don’t substitute all regular whole wheat flour, as the muffins will come out dense and grainy. To make gluten-free buttermilk muffins, use a gluten-free flour mix, such as Bob’s Red Mill 1-to-1 Gluten-Free Flour.
  • Spices: use cinnamon, pumpkin pie spice, apple pie spice, ginger, cardamom, cloves, nutmeg, allspice, or a combination. Some spices, like cloves, are stronger than others, so adjust quantities as appropriate; 1 teaspoon of pure cloves would be too much!
  • 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. 
  • Shredded or Pureed Fruits or Vegetables: use any combination of shredded or pureed fruits and vegetables. Shredded zucchini, shredded carrots, mashed ripe bananas, canned pumpkin, or pureed butternut squash are all great options. Unsweetened applesauce works too, but it has a very high moisture content, so the muffins won’t rise as well.
  • 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, 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 whole wheat muffins, substitute the eggs with flax eggs. To make two flax eggs, mix 2 Tablespoon ground flaxseeds with 6 Tablespoons of water and let it rest for 10 minutes. Eggs help leaven the muffins, so a vegan version might not be quite as fluffy.

Base Recipe Variations

Remember that this is a base recipe, so the goal is for you to customize it to your taste! Keep it simple or spruce it up!

Use these additional ingredients for even more flavor and texture.

  • Dark Chocolate Chips: substitute mini or semi-sweet chocolate chips for best flavor. We don’t recommend using milk or white chocolate, as these are not generally healthy options.
  • Unsweetened Coconut
  • Dried Fruit: use any dried fruit – raisins, chopped figs, cranberries, cherries, and dried blueberries all work well. If using larger fruits such as dried apricots, figs, or prunes, dice into smaller pieces before adding.
  • Nuts or Seeds: chopped or sliced walnuts, almonds, pecans, sunflower seeds, pumpkin seeds, hemp seeds, or even flax seeds provide great texture and nutrition. Toast nuts before adding for even better flavor.
  • Old Fashioned Oats: substitute quick oats. Don’t use steel cut oats, as these have to be cooked in water for digestibility.
  • Vanilla Extract: substitute almond, coconut, or lemon extract.
  • Cocoa Powder
  • Lemon or Orange Zest

Want to make mini 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 batter works for quick bread too! To make a whole wheat quick bread loaf, 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?

Check out some of our favorite variations, then have fun exploring other flavors, ingredients, and textures to YOUR taste! 

Equipment Recommendations

Use these kitchen tools for recipe success:

Find all of our favorite kitchen tools here!

Are these muffins healthy?

Most pre-made muffins or store bought mixes contain way too much added sugar. Some even contain 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, fruits and/or vegetables, 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.

Fruits and Vegetables

Fruits and vegetables provide fiber, vitamins, minerals, and phytonutrients. Consuming a variety of natural colors is ideal. Incorporating vegetables into a breakfast, snack, or dessert recipe is an easy way to help you meet your daily vegetable needs!

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 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 Muffins

Because these are moist 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 Wheat Quick Bread Base Recipe

Overnight Oats Base Recipe

Whole Grain Pancakes Base Recipe

Baked Oatmeal Cups Base Recipe

Stovetop Oatmeal Base Recipe

three whole wheat muffins on a plate with a pan of muffins in the background

Whole Wheat Muffins Base Recipe

This is one of our base recipes. 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


Base Recipe

  • 1 ½ cups white whole wheat flour*
  • 1-2 teaspoons spice(s)
  • 1 teaspoon baking powder
  • 1 teaspoon baking soda
  • ½ teaspoon kosher salt
  • 1 cup shredded or pureed fruits or vegetables
  • ½ cup buttermilk
  • ½ cup packed brown sugar
  • ¼ cup canola oil
  • 2 large eggs

Mix-ins to YOUR taste

  • ½ cup dark chocolate chips
  • ¼-½ cup unsweetened coconut
  • ¼-½ cup dried fruit
  • ¼-½ cup toasted chopped or sliced nuts or seeds
  • ¼-½ cup old fashioned oats
  • 1-2 Tablespoons cocoa powder
  • 1 teaspoon lemon or orange zest
  • 1 teaspoon vanilla extract


  • Preheat oven to 350°F. Prepare a 12-cup muffin pan with nonstick spray or muffin liners.
  • In a large bowl, gently whisk flour, spices, baking powder, baking soda, and salt. Add additional mix-ins (except vanilla) to flour mixture. Toss to evenly coat.
  • In a separate medium bowl, whisk together fruit/vegetable puree or shreds, buttermilk, brown sugar, oil, eggs, and optional vanilla.
  • Add liquid ingredients to flour mixture. Using a spatula, fold ingredients until just 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.
If you used all of the mix-ins, the recipe will make more than 12 muffins. Bake in reusable silicone muffin liners on a small sheet pan or cake pan.
Check out these recipes for flavor inspiration!
Carrot Orange Cranberry
Banana Buttermilk
Apple Walnut
Sweet Potato Almond Butter
Pumpkin Banana
Keyword Whole Wheat Muffins

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