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    Home » Resources

    20 Tips For Making the Best Whole Wheat Muffins

    Published: Apr 16, 2024 by WholeWheatKitchen · This post may contain affiliate links · Leave a Comment

    Muffins are such a versatile baked good, they can be eaten for breakfast, snack, or a dessert. Making them with whole wheat flour is a good way to up the nutritional value, making them even more versatile and you can feel good about eating them.

    They are one of the easiest things to make with whole wheat flour, especially if you are just starting with whole wheat flour. We have been making muffins with 100% whole wheat flour for decades now and have accumulated a list of all our tips to achieve moist, tall, domed and delicious muffins made with 100% nutritious whole grain flour.

    Collage of whole wheat muffins.

    Recipes for the photo above starting at the top, left to right (all made with 100% whole wheat flour):

    • Zucchini
    • Chocolate banana
    • Pumpkin
    • Carrot
    • Lemon poppy seed
    • Cranberry orange

    Muffin Tips

    1. Bake at 400°F

    Baking muffins at a high temperature will make them rise up more and make that glorious muffin dome. Some recipes will have you bake at a really high temperature, like 425°F for a few minutes and then reduce the temperature down to 350°F. We prefer to bake them at 400°F the whole time. That way you get that nice rise but you don’t run the risk of forgetting to lower the temperature and burning the muffins. 

    Graphic showing the differences baking temperature has on muffins.
    1. Use the right kind of whole wheat flour

    Soft white wheat, spelt or hard white wheat are the best types of wheat to use for muffins. Because soft white wheat has a low protein content it makes super light and fluffy muffins. Spelt flour will also produce a light and fluffy texture, although it has a darker color and a stronger flavor. Hard white wheat makes great muffins as well. The texture will be just a tad bit heavier but still delicious.

    1. Use butter to grease the muffins cups

    Use a pastry brush to paint the muffin cups with softened butter before filling with batter. We have found this is the best way to get the muffins out of the tin after baking. You can use cupcake papers with some muffin recipes, but a lot of them stick to the papers.

    1. Fill the cups almost full

    If you want tall, domed muffins, fill your muffin tins almost all the way full.

    1. Weigh ingredients

    Using a kitchen scale to measure your ingredients will help you achieve more consistent results. All our recipes are tested using weight measurements for accuracy.

    1. Reduce baking time if using convection mode 

    If your oven doesn’t auto adjust the temp when using convection mode then you will need to reduce the baking time by 2-3 minutes. 

    1. Bake in the center of the oven

    We have found that muffins rise taller if they are baked in the center of the oven.

    1. Use fresh flour

    Whole wheat flour(s) are prone to going rancid because of the oil in the germ that is present in most whole wheat flour. Using the freshest flour possible will give you the best results. Grinding your own flour is the best way to ensure you are using fresh flour. Or buy a high quality store bought flour and store it in the refrigerator.  

    1. Don’t be afraid to stir the batter

    Whole wheat flour, especially fresh milled whole wheat flour can benefit from a little vigorous stirring (soft white wheat in particular).

    1. Have the right batter consistency

    You’ll want the batter to be a little on the thicker side, but not too thick (you should still be able to pour the batter but it should be thicker than cake batter) especially if you have mix-ins like chocolate chips or blueberries.

    Whole Wheat Muffin Recipes

    • A pile of lemon poppy seed muffins with a bite taken out of one.
      Easy Whole Wheat Lemon Poppy Seed Muffins
    • Banana muffins in a bowl lined with a tea towel.
      Low Sugar Banana Muffins (whole wheat)
    • A pumpkin muffins sitting on top of a muffin tin.
      Healthy Low Sugar Pumpkin Muffins with Yogurt
    • Top view of baked muffins in a muffin tin.
      The Best Moist Carrot Cake Muffins (made healthier)

    More muffin recipes

    1. Don’t over bake, check with a toothpick 

    Check your muffins by poking a toothpick into the center of a muffin, it should come out clean or with a few moist crumbs. Chocolate muffins are better taken out with a few moist crumbs on the toothpick.

    Most standard size muffins will take between 14-20 minutes when baked at 400°F. Muffins bake faster in dark colored pans and take a little longer in light colored pans.  

    1. How to remove muffins from the tin

    To remove muffins that are a little stubborn, while the muffins are still warm from the oven, tilt the muffin tin up and tap each edge of the pan on the counter, they should release after a few taps.

    1. Store with a paper towel to prevent soggy tops

    To prevent muffins from getting soggy tops in storage, place a paper towel over the muffins in the storage container.

    1. Rinse frozen fruit

    If you’re using frozen fruit in your muffins, rinse the fruit under cold water until the water runs clear (or almost clear) this will help keep the fruit from turning your batter a funny color. 

    1. Test leaveners

    If you are having problems with your muffins not rising properly, the first thing to do is test your leaveners to see if they are still active. 

    1. Use double acting baking powder

    Double acting baking powder is activated twice, when it is mixed with a liquid and when it gets hot. This ensures your muffins will get the best rise possible. Using double acting baking powder is a must if you’re letting your batter rest overnight.

    1. Use an ice cream scoop to fill cups

    Use a trigger release scoop for an easy, convenient way to fill muffin cups. A 2 ounce or ¼ cup scoop is usually the perfect amount of batter for a standard size muffin cup.

    1. Preheat oven completely

    Make sure the oven is completely preheated before you place the muffins into the oven. Immediate high heat is one of the most important elements to get tall muffins.

    1. Don’t cool in the tins

    Remove the muffins from the pan just a few minutes after they come out of the oven and place them on a cooling rack. This will prevent the edges of the muffins going soggy.

    1. Use oil 

    We use oil in our muffin batters most of the time because oil makes more moist baked goods. There are a few occasions where we use butter for flavor like in our peach muffins, apple streusel muffins and chocolate chip muffins.

    More Resources

    • A burlap bag of wheat berries with some wheat stalks and a bowl of wheat flour.
      Getting Started with Whole Wheat Flour
    • How to Make Flour From Wheat (grinding your own flour)
    • A handful of whole wheat flour.
      Whole Wheat Flour Buying Guide (where to buy whole wheat flour)
    • Graphics of grin mills.
      How To Choose A Grain Mill to Buy

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    Hi, we're Jessica and Merissa. We are here to share recipes and teach people how to bake more nutritious breads and goodies by using whole wheat flour.

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