Wheat Germ Muffins (Nutritious & Delicious Muffins)

These wholesome wheat germ muffins are light, fluffy, and moist, with a lovely crunch on top. They’re delicious on their own and also a great base for all your favorite spreads. Enjoy this delicious fiber-filled recipe as breakfast muffins or as a quick snack!

This wheat germ muffin recipe has quickly become our new favorite muffin! The first time we made these was as a way to use up wheat germ purchased for my popular whole wheat zucchini bread recipe.  

We thought they were such good muffins that we kept making them with various tweaks to the original recipe each time. After a lot of recipe testing, I landed on this irresistibly soft and fluffy muffin recipe, with a slightly hearty texture and (very) subtle apple-cinnamon flavor. And they’ve been a part of our go-to breakfast recipes for years! The applesauce and spices aren’t overpowering, though; the nutty flavor from the wheat germ really shines through!  

Muffins with wheat germ might not sound as tempting as double chocolate muffins, blueberry muffins, or pumpkin streusel muffins, but I guarantee that once you try one, they’ll become your favorite as well! We personally love to serve wheat germ muffins warm with a nice spread of butter and a drizzle of honey. 

So next time you’re wanting a delicious homemade muffin, this recipe is a great way to satisfy your craving!

Benefits of Wheat Germ

Wheat germ contains various vitamins and minerals, being especially high in vitamin e. It’s also a good source of dietary fiber and plant-based protein. Due to its nutritional content, wheat germ may support the immune system and digestive system. This makes recipes with wheat germ excellent choices for anyone prioritizing wellness and nutrition.   

Ingredients Needed

• Large Egg. Using whole eggs add structure to muffin batter and help hold the ingredients together. They add a little extra protein to our wheat germ muffins, too!  
• Vegetable or canola oil. I prefer vegetable oil or canola oil in muffin recipes because both oils have a neutral flavor. This means you won’t taste the oil in the muffins. Oil adds moisture and gives the muffins a soft texture.    
• Unsweetened applesauce. I love including applesauce in my muffin recipes because it adds natural sweetness and moisture. Applesauce acts like fat in baked goods, but doesn’t actually add any extra fat! Additionally, it decreases the amount of processed sugar in the recipe. 
• Milk. I use skim milk or 2% dairy milk. But you can also use any unsweetened non-dairy milk of choice. Milk is added for moisture, giving the muffins a nice, tender texture.    
• Brown sugar. Brown sugar adds a caramel-like sweetness to the wheat germ muffins. Although applesauce provides natural sugar, it isn’t quite enough. A small addition of brown sugar is needed to boost the overall flavor of the muffins. 
• Salt. A pinch of salt brings out the sweetness in the muffins and adds depth of flavor to the overall recipe. 
• Cinnamon and nutmeg. When combined with applesauce, cinnamon and nutmeg add subtle, fall-like flavors. The apple-cinnamon flavor isn’t overpowering, though!   
• Baking powder and baking soda. The combination of both baking powder and baking soda forms perfectly domed muffin tops! These leavening agents work together to create a reliable and consistent rise every single time.  
• Wheat germ. Our star ingredient! Wheat germ imparts a slightly nutty, earthy taste to baked goods. It’s also nutrient-dense, adding essential vitamins, minerals, and fiber to our recipe.    
• All-purpose flour. All-purpose flour gives the muffins a nice and light texture without making them too dense.  
• Whole wheat flour. Whole wheat flour provides the hearty texture wheat germ muffins are known for. It’s high in fiber as well, which is an added bonus!  
• Turbinado sugar. Turbinado sugar is coarse, with larger crystals and a light tan color. The large crystals add a delightfully sweet crunch to the top of the muffins. 

See recipe card below for a full list of ingredients and measurements. 

Recipe Variations and Substitutions

• Replace the whole wheat flour. Substitute whole wheat flour with all-purpose flour if you don’t have whole wheat flour on hand (or if you just prefer to use all white flour). You’ll miss out on some of the extra texture whole wheat flour provides, but the recipe will still turn out perfectly fine without it. 
• Add a splash of vanilla extract. For added depth of flavor, feel free to add 1-2 teaspoons of vanilla.
• Add mix-ins. While I haven’t tested this recipe with different mix-ins, I think you could add up to 1 cup of flavor additions, such as blueberries, raspberries, or chocolate chips. Blueberry wheat germ muffins are commonly found at coffee shops and bakeries!   

Step-by-Step Instructions

Preheat your oven to 425°F. Generously spray your muffin tin with cooking spray and set aside.

Beat the egg with the oil, applesauce, milk, and brown sugar in a large bowl.

Add the salt, cinnamon, nutmeg, baking powder, baking soda, wheat germ, all-purpose flour, and whole wheat flour. If desired, you can pre-mix your dry ingredients in a separate bowl and then add the flour mixture to the wet ingredients.

Slowly mix in the dry ingredients until a batter is formed. Stir until just combined, being careful not to over-mix. A few lumps are ok!   

Divide the batter between the muffin cups of a 12-cup standard-sized muffin tin.   

Add a generous sprinkle of turbinado sugar to the top of each muffin. The sugar adds a nice crunchy texture and a little extra sweetness.  

Bake the wheat germ muffins for 15-17 minutes, until golden brown on top and a toothpick inserted into the center comes out clean. A few crumbs on the toothpick are ok! 

Let the muffins cool in the muffin tin for a few minutes, then transfer them to a wire rack to cool completely. 

We enjoy wheat germ muffins while they’re still warm from the oven, or cooled to room temperature. They’re delicious both ways! 

How to Use Wheat Germ

Don’t let your package of wheat germ go to waste! We love using wheat germ in this whole wheat zucchini bread recipe and adding it to yogurt, smoothies, cereal, and granola is an easy way to incorporate wheat germ into your day-to-day meals. Additionally, wheat germ is a fantastic substitute for bread crumbs in meatballs and meatloaf. It’s a breadcrumb alternative for breaded chicken as well!    

Recipe FAQs

Is wheat bran the same as wheat germ?

No, while both come from a part of the wheat kernel, wheat bran comes from the outer layer of the wheat kernel, while wheat germ is derived from the inner portion of the wheat kernel. Wheat bran and wheat germ have slight differences in taste and distinct differences in texture. Wheat bran has a flakey texture, and wheat germ has a crunchy texture.  

Can I use wheat germ instead of flour?

Wheat germ can be substituted for a small portion of flour in some recipes. According to the baking experts at Bob’s Red Mill, wheat germ can replace up to ½ cup of flour in most cookie, muffin, and bread recipes.   

Can you toast wheat germ?

Yes, toasting wheat germ enhances its nutty flavor and crunchy texture. To do so, spread a thin layer of wheat germ out on a baking sheet, and bake at 350°F for about 5 minutes. Alternatively, wheat germ can be toasted in a skillet on the stovetop over low heat.   

What does wheat germ do in baking?

Wheat germ is added to baked goods for three main reasons: flavor, texture, and nutrition. It adds a slightly nutty flavor, a hearty texture, and a boost of vitamins, minerals, and fiber.