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Photo of three healthy cinnamon apple muffins stacked upon each other with a bite taken out of the top muffin showing chunks of apples in the middle of the muffin

Healthy Cinnamon Apple Muffins

Course Breakfast
Prep Time 20 minutes
Cook Time 17 minutes
Servings 9 muffins



  • 1 cup (125 grams) whole spelt, whole wheat flour, all-purpose flour or for a gluten-free version, use 1 cup (138 grams) Bob's Red Mill Gluten-free 1-to-1 Baking Flour
  • 3/4 teaspoon baking soda
  • 1/2 teaspoon baking powder
  • 1/4 teaspoon salt
  • 1 teaspoon cinnamon
  • 1/2 teaspoon nutmeg
  • 1/4 teaspoon allspice, optional
  • 1 large (50 grams, out of shell) egg
  • 1/3 cup (106 grams) honey
  • 1/4 cup + 2 tablespoons (90 ml) olive oil* or another neutral-tasting oil (if you want to use coconut oil, use refined for no coconut taste)
  • 1 teaspoon vanilla extract
  • 1/4 cup (60ml) plain yogurt or buttermilk (use dairy-free yogurt or homemade dairy-free buttermilk** for a dairy-free version)
  • 1 cup (120 grams) diced apple, preferably from baking apples like Granny Smiths (I needed one medium / large apple and diced chunks about 1/4" in size)


  • 1/3 cup (45 grams) whole spelt, whole wheat flour or all-purpose flour
  • 1/2 cup (100 grams) brown sugar or coconut sugar
  • 2 tablespoons (28 grams) melted unsalted butter
  • 2 teaspoons cinnamon
  • 1/8 teaspoon salt


  • 1/2 cup (69 grams) Bob's Red Mill Gluten-free 1-to-1 Baking Flour
  • 7 tablespoons (88 grams) brown sugar or coconut sugar
  • 3 tablespoons + 1 teaspoon (47 grams) melted coconut oil
  • 2 teaspoons cinnamon
  • 1/8 teaspoon salt


  • Mix the streusel ingredients in a small bowl until well combined. ***
  • Preheat the oven to 350°F / 175°C. Line a muffin tin with 9 muffin liners.
  • In a medium bowl, whisk together the dry ingredients (flour through salt).
  • In another bowl, mix the wet ingredients (egg through yogurt).
  • Add the flour mix to the wet mix. It just needs to be combined, so be careful not to overmix.
  • Then fold in the apples, being careful not to overmix.
  • Fill the liners with the batter, filling them about 2/3 full.
  • Divide the streusel between the muffins. If you like being exact, that's 20 grams per muffin for the wheat version and 23 grams for the GF version. It's a little more than a tablespoon.
  • Bake for about 15 – 17 minutes or until a toothpick comes out clean. I needed 15 for the wheat version and 17 minutes for the GF version. But all ovens vary so have an eye on them.
  • Let the muffins cool for 5 minutes and then turn out onto a wire rack to cool.
  • When the muffins are completely cooled, place them in an airtight container and store at room temperature for up to 4 days. Anything past that, store in the refrigerator.


Please read the post for more tips and answers to the most common questions!

* If you want to make the gluten-free version and eat them straight from the oven and have no olive oil taste, you'll likely want to use a lighter olive oil and not extra-virgin. See post for more notes on olive oil type. 
** To make dairy-free buttermilk, add 3/4 teaspoon of lemon juice, white vinegar or apple cider vinegar to a 1/4-cup measuring cup. Fill with dairy-free milk and let sit for 5 minutes.
*** If you don’t want to make the streusel, add some cinnamon sugar (1 tablespoon raw sugar or granulated sugar + 1 teaspoon cinnamon) to the top of the muffins. It adds a wonderful crust and a little extra sweetness.