Recipe | Apple Cinnamon & Quinoa Muffin Top Cookies

Apple Cinnamon and Quinoa Muffin Top Cookies

Apple Cinnamon & Quinoa Muffin Top Cookies
When deciding on a name for these cookies, I was all excited thinking I had come up with something totally original–muffin top cookies! And then I did a search for the term and, sure enough, lots of people make muffin top cookies. But! I’m the only one that’s made Apple Cinnamon & Quinoa Muffin Top Cookies! So that’s something, right?

This recipe is really a happy accident. I wanted to make a breakfast cookie that was low in calories and fairly substantive and healthy. I decided to put quinoa in the cookies, but I wasn’t sure how to go about doing it, so I adapted a recipe from Bon Appetit. One of the changes I made was to sub out white whole wheat flour for whole wheat pastry flour. In my mind, I couldn’t see much of a difference between the two–since I like whole wheat, I’ve never been one to buy the white wheat stuff.

Apple Cinnamon & Quinoa Muffin Top Cookies on Rack
Well! It turns out that using pastry flour in cookies makes them cakey. I was expecting to open the oven and find chewy cookies waiting for me and instead, I had something that looked more like muffin tops. I resigned myself to buying the ingredients again and trying another day, but once they cooled down enough for me to try one, I was surprised to find that they were really good. I gave one to my husband and he helped himself to several more. So it all turned out okay!

Although it’s kind of hard to tell from the pictures, these cookies puff up like the tops of muffins when they’re baking in the oven. So you get all the fresh-baked goodness of muffin tops, without that pesky stump. With the whole wheat flour, oats, and quinoa, these make a great cookie to have with breakfast or as an afternoon snack.


Apple Cinnamon & Quinoa Muffin Top Cookies

Apple Cinnamon & Quinoa Muffin Top Cookies with Honey

Muffin-like cookies made with diced apples, quinoa, and plenty of cinnamon. They taste even better when drizzled with a little bit of honey before serving! Adapted from Bon Appetit’s Almond Cranberry Quinoa Cookies.

  • Prep Time: 15 minutes
  • Cook Time: 15 minutes
  • Total Time: 30 minutes
  • Yield: 36


  • 1 1/2 c. whole wheat pastry flour
  • 1 tsp. Kosher salt
  • 1/2 tsp. baking powder
  • 1/2 tsp. baking soda
  • 2 tsp. cinnamon
  • 1/2 c. unsalted butter, softened
  • 1/4 c. sugar
  • 1/4 c. light brown sugar, packed
  • 1/4 c. honey
  • 2 large eggs
  • 1 tsp. vanilla extract
  • 1 c. cooked quinoa, cooled
  • 1 c. old-fashioned oats
  • 1 c. apple, diced (about 1 medium apple)


  1. Preheat oven to 375 degrees. Line two baking sheets with parchment paper.
  2. In a medium mixing bowl, whisk together flour, salt, baking powder, baking soda and cinnamon. Set aside.
  3. In a large mixing bowl, cream butter, sugars, and honey with a hand mixer until light and fluffy (about 3 minutes). Beat in eggs and extract; continue beating for 2 minutes. Gradually beat in flour mixture. Fold in quinoa, oats, and apple.
  4. Spoon two-tablespoon sized balls of dough onto baking sheets, spaced one inch apart. Bake until golden brown, 12-15 minutes. Cool on wire racks.


  • Serving Size: 1 cookie

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Oh, these look soooo good! I love that you have quinoa in these and that they are so low in points. What a great addition to my life these will be!

I love finding other uses for quinoa, like in baked goods. And the combination of apples and cinnamon in a soft and puffy cookie sounds like the perfect on-the-go breakfast to me!

The important thing about quinoa is to rinse it before you use it, otherwise it’s bitter! I like it because it’s a good source of protein and since it’s a grain, you can use it in place of rice, couscous, etc.

Oh, happy “mistakes”! These look so tasty and not terribly unhealthy! I love quinoa, so these are going to be added to my “make this “list. Hey, it’s a long list, but I’ll get to everything on there! 🙂

I miss chatting with you more! Hope all is well.

YES! Although on the other hand, since muffin top cookies are already a thing, at least that means people will probably be searching for them. Sometimes when an idea is too original, you get no traffic on it!

Do you combine your whole wheat flour with white flour? That’s what I usually do because I’ve read that works best, but I’d really like to sub out the whole amount of white flour with whole wheat.

Is that one cup of quinoa that is then cooked or one cup after cooking?

The recipe looks so yummy that I’m dying to try it!

What other type of flour could you sub for whole wheat (wheat allergy) oatflour? I would also love to attempt substituting sugar with truvia. Thoughts?

I’m not sure; I don’t bake gluten- or sugar-free, so I’m not familiar with the different substitutes that are used. I’m sorry I can’t help–I don’t want to guess and tell you the wrong thing and have it turn out terrible!

I know this recipe was posted a few years ago, but I happened upon it when I wanted to use up an apple I had and make healthier treat for my coworkers. I must say, this was a hit! I hadn’t anticipated how much they would expand in the oven, so they were a bit overwhelming in size, but I heard no complaints : ) Thank you for posting this!

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