Whole Wheat Rye Muffins With Apples And Raisins

Fluffy and soft, topped with crunchy brown sugar and cinnamon streusel, these whole wheat rye muffins with apples and raisins are an irresistible treat this fall. Not only are they delicious, but they only use 100% whole-wheat rye flour and are so easy to make.

A basket full of apple and raisin rye muffins.

The nutty flavors of rye merge perfectly with the sweet and tart apple aromas. The raisins, cinnamon, and brown sugar, all complement each other and add an extra layer of yummy fall flavors.

Whether you enjoy them for breakfast or as an afternoon snack, these apple muffins are sure to become a favorite in your household. Get ready to indulge in a delicious treat that will leave you feeling satisfied and nourished.

An apple and raisin rye muffin

Even though they are made with only whole wheat rye flour, these muffins are soft and fluffy just like their white flour counterpart. All you need is a few simple tweaks in the recipe, and you will be impressed with the results.

Ingredients needed for the whole wheat rye muffins:

Ingredients needed to make apple and raisin rye muffins.
  • cooking apples (any type of apple that holds shape while cooking will work)
  • raisins (or sultanas)
  • whole wheat rye flour (dark rye flour)
  • eggs
  • white sugar (I used unrefined cane sugar)
  • brown sugar 
  • baking powder
  • baking soda
  • butter
  • cinnamon
  • a pinch of salt

Make sure to follow the exact ingredients list in the recipe card.

An apple and rye muffin nestled in between apple tree branches

How to make the perfect whole wheat apple muffins:

  • Preheat your oven to 180°C (356°F)
  • Peel and chop your apples into cubes.
  • Place them in a saucepan with a splash of lemon juice (this will stop the apples from oxidizing).
  • Cook them on low heat until they are softened (not mushy). Keep an eye on the pan and stir regularly to avoid sticking and burning.
  • Let the apples cool off.
  • Separate the egg yolks from the egg whites.
  • In a large bowl, cream the egg yolks with the sugars.
Photo collage of the process of making apple and raisin rye muffins.
  • Add in the cinnamon, baking powder, baking soda, and salt.
  • Pour in the melted butter and mix well. Make sure the butter has cooled off before adding it in, to avoid cooking the eggs.
  • Add 1 cup of the dark rye flour and mix it in until well incorporated.
  • In a separate bowl, whisk the egg whites to stiff peaks. Use an electric mixer for this.
  • Fold in the whisked egg whites in the muffin butter. Use gentle folding motions to avoid losing that fluffy and airy texture.
Photo collage of the process of making apple and raisin rye muffins.
  • Add in the chopped apples and raisins. Mix them in gently.
  • Now it’s time to add the rest of the flour. I recommend you do this gradually as you might not need the whole amount of flour or need more than that. This depends on the flour you use, the size of the eggs, and the type of apples used in the recipe. The end result should be a normal muffin batter. Not too thin and runny, nor too thick and dry.
  • Prepare your muffin tray with paper muffin cups (or reusable silicone ones).
  • Add in the muffin batter. I recommend you fill them up halfway and then equally add up the rest of the batter. This way you make sure all the muffins are the same size.

Make the streusel (crumb topping):

  • In a large bowl, mix in the brown sugar, cinnamon, dark rye flour, and cold butter.
  • With your hands crumble all the ingredients together.
  • This results in a clumpy, sand-like texture.
  • Top the muffins with the streusel.
  • Add it in gradually to ensure an equal spread on all the muffins.
Muffin batter in a paper cup ready to be baked
  • Bake the muffins at 180°C (356°F) for about 25 minutes. They should have risen well and be golden brown on top.
  • Let the muffins cool off in the tin for about ten minutes or so. After that, you can remove them and place them on a wire rack to completely cool off.
  • Serve and enjoy!
Apple muffins in a muffin tin.

Pro tips:

  • Make sure you use cooking apples for this muffin recipe. These apples will hold their shape better and not become mushy. I used Braeburn, but Granny Smith, Fuji, or Honeycrisp should work.
  • Don’t overmix the flour as this will develop gluten more, which can result in dense muffins.
  • Don’t skip the egg white whisking step. It is important to the overall fluffy texture of the baked muffins. Folding them gently in the batter is also key to this.
  • The brown sugar and cinnamon streusel is optional but I highly recommend it for an extra crunch, sweetness, and flavor.
A muffin out of the muffin tin

How to store and freeze the muffins:

  • Allow them to cool off completely before storing or freezing.
  • If you wish to store them at room temperature, placing the muffins in a container with a loose lid should suffice. For a longer storage time, place them in the fridge in an airtight container for up to a week.
  • These apple and raisin muffins also freeze well. Place each individual muffin in a zip-tie bag and freeze them for up to a month. They defrost really quickly at room temperature. So, perfect for lunch boxes or snacks on the go.
A half eaten apple and raisin muffin

Other delicious dessert recipes to entice you:

Simple Almond And Rye Cookies

Easy Plum Cake With Meringue Dough

Sourdough Spiced Peanut Butter Cookies

A wire basket with apple rye muffins.
A basket full of apple and raisin rye muffins.

Whole Wheat Muffins With Apples And Raisins

AndreeaB
These delicious apple and raisin whole wheat muffins are so fluffy and soft you won't believe they are made without white flour.
5 from 4 votes
Prep Time 20 minutes
Cook Time 25 minutes
Total Time 45 minutes
Course Breakfast, Dessert, Snack
Cuisine German-Austrian
Servings 12
Calories 175 kcal

Equipment

  • 1 Muffin Tin
  • 1 Electric Mixer

Ingredients
  

  • 1 cup cubbed and cooked apples (about 2 medium-sized apples) I used Braeburn but any cooking apples should work
  • 1 and 1/2 cups dark rye flour (whole wheat rye flour) divided
  • 1/2 cup raisins (or sultanas)
  • 2 eggs (room temperature)
  • 1/3 cups melted butter
  • 1/2 cups caster sugar I used unrefined caster sugar
  • 1/3 cups brown sugar
  • 1 tsp cinnamon
  • 1 tsp baking soda (bicarbonate of soda)
  • 2 tsp baking powder

For the streusel

  • 1 tbsp dark rye flour
  • 1/4 cup brown sugar
  • 1/2 tsp cinnamon
  • 1 tbsp butter (room temperature)

Instructions
 

  • Preheat your oven to 180°C (356°F)
  • Peel and chop your apples into cubes.
  • Place them in a saucepan with a splash of lemon juice (this will stop the apples from oxidizing).
  • Cook them on low heat until they are softened (not mushy). Keep an eye on the pan and stir regularly to avoid sticking and burning.
  • Let the apples cool off.
  • Separate the egg yolks from the egg whites.
  • In a large bowl, cream the egg yolks with the sugars.
  • Add in the cinnamon, baking powder, baking soda, and salt.
  • Pour in the melted butter and mix well. Make sure the butter has cooled off before adding it in, to avoid cooking the eggs.
  • Add 1 cup of the dark rye flour and mix it in until well incorporated.
  • In a separate bowl, whisk the egg whites to stiff peaks. Use an electric mixer for this.
  • Fold in the whisked egg whites in the muffin butter. Use gentle folding motions to avoid losing that fluffy and airy texture.
  • Add in the chopped apples and raisins. Mix them in gently.
  • Now it's time to add the rest of the flour. I recommend you do this gradually as you might not need the whole amount of flour or need more than that. This depends on the flour you use, the size of the eggs, and the type of apples used in the recipe. The end result should be a normal muffin batter. Not too thin and runny, nor too thick and dry.
  • Prepare your muffin tray with paper muffin cups (or reusable silicone ones).
  • Add in the muffin batter. I recommend you fill them up halfway and then equally add up the rest of the batter. This way you make sure all the muffins are the same size.

Make the streusel (crumb topping):

  • In a large bowl, mix in the brown sugar, cinnamon, dark rye flour, and cold butter.
  • With your hands crumble all the ingredients together.
  • This results in a clumpy, sand-like texture.
  • Top the muffins with the streusel.
  • Add it in gradually to ensure an equal spread on all the muffins.
  • Bake the muffins at 180°C (356°F) for about 25 minutes. They should have risen well and be golden brown on top.
  • Let the muffins cool off in the tin for about ten minutes or so. After that, you can remove them and place them on a wire rack to completely cool off.
  • Serve and enjoy!

Notes

  • Make sure you use cooking apples for this muffin recipe. These apples will hold their shape better and not become mushy. I used Braeburn, but Granny Smith, Fuji, or Honeycrisp should work.
  • Don’t overmix the flour as this will develop gluten more, which can result in dense muffins.
  • Don’t skip the egg white whisking step. It is important to the overall fluffy texture of the baked muffins. Folding them gently in the batter is also key to this.
  • The brown sugar and cinnamon streusel is optional but I highly recommend it for an extra crunch, sweetness, and flavor.

Nutrition

Serving: 75gCalories: 175kcal
Keyword apple and raisins muffins, apple and rye muffins, fluffy rye muffins, whole wheat muffins, wholewheat rye muffins
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7 Comments

  1. These look so yummy! Planning to make these for breakfasts for the days I work. I’ve got everything but the rye flour to make these for the upcoming (short) week. 😀

  2. 5 stars
    I can’t wait to make these! And I saw a recipe for peanut butter cookies. ❤️ I can’t wait for your next post!

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