Pineapple Pecan Cupcakes {Gluten-Free}

By Sara McGlothlin

I have a confession to make: when I started writing this recipe, I didn’t intend to make pineapple pecan cupcakes. Have you ever heard of pineapple pecan cupcakes with a cream cheese frosting? I haven’t. But baking is my art, and this is a prime example of how I created something from nothing. I started out wanting to make hummingbird cupcakes (and I still plan to in the near future), but I didn’t have banana on hand, so I called an audible. The incorporation of mashed banana makes them hummingbird cupcakes. Without it, they are simply pineapple pecan cupcakes. You can even call them muffins. They are nutritious enough to be muffins. 

These cupcakes do have a backstory. The other day my husband brought a pineapple home from the grocery store. “Look what I got!” he exclaimed. With how much pre-cut pineapple you can find in the store these days, I don’t think I have bought (or sliced) a whole pineapple since I was a preschool assistant right after college. One of my student’s moms brought a whole pineapple as his snack contribution for the week (no cheddar bunnies for her child!). This was before I was familiar with YouTube (or maybe YouTube wasn’t a thing in 2008? I guess to me it wasn’t), and I remember going home and looking up how to cut a pineapple. It is a hidden talent I hold to this day, thank you very much. While I was cutting the pineapple, I had every intention of throwing the pieces in a plastic bag and freezing them for smoothies. But then I paused, and the idea of cupcakes popped into my mind (as it tends to do). Fast forward to prepping all of the ingredients for hummingbird cupcakes and then realizing it was about the only time I didn’t have ripe banana in my fruit basket. I made these pineapple pecan cupcakes instead. I really wanted to serve them for dinner that night as we were having company, so I made it work. If you really wanted to, you could call them banana-free hummingbird cupcakes. Tomato, tomahto.

Aside from adding flavor, fruit purees in Healthified baking add moisture and natural sweetness. You will find purees in many forms in my recipes, from applesauce, to avocado, to pumpkin to butternut squash. As you could have guessed, banana is also a popular one, but sometimes you don’t want your cake or cupcake to taste like banana, so you must find something more neutral. These cupcakes are supposed to have a pineapple-forward flavor profile, and I am so happy with the way they turned out. An added bonus: my two-year-old loves them, and when I can hide a fruit or vegetable into a baked good I call it a win. 

The last thing I will say: for convenience, you can use a 14-ounce can of crushed pineapple. I had fresh pineapple on hand that I had cut up days prior (see husband’s proud moment above). After measuring out 14 ounces on my kitchen scale, I blended it in my food processor until more of a crushed consistency. It equaled about 1½ cups. This worked well! You could also get a container of pre-cut pineapple that so many grocery stores have these days and put it through the same process. 

Planning and prep

I did bring my eggs to room temperature before I began baking. This is a good rule of thumb, because room temperature ingredients cream more consistently than cold ingredients. I will be honest: I rarely do this unless I am also working with butter or coconut oil/milk. I can be a lazy baker. But I have found that a recipe works better when I do take the time to bring certain ingredients to room temperature, and I remembered to do it this time around. If you want to play it safe, take out two eggs about an hour before you start this recipe. 

The icing on the (cup)cake is the cream cheese frosting. You can also use a simple vanilla frosting (homemade or store bought. I like Simple Mills brand). If you know how to pipe, it does make it pretty, but I also simply spooned some frosting on top and smoothed it down. I show the difference below. As always, if you call your baking creation complete before frosting, its delicious enough on its own!

Pineapple Pecan Cupcakes {Gluten-Free}

A fruity and nutty nutritious cupcake made with a gluten-free flour combination. These cupcakes would be perfect for a mid-morning brunch, bridal or baby shower. Use the frosting or enjoy them without.
Prep Time 20 minutes
Cook Time 20 minutes
Cooling Time 1 hour
Total Time 1 hour 40 minutes
Course Dessert
Servings 20 servings


  • muffin tin
  • Hand beater or stand mixer


For the cupcakes

  • ½ cup full-fat coconut milk or unsweetened dairy-free milk of choice I used almond milk
  • 1 teaspoon white vinegar or apple cider vinegar
  • cups brown rice flour
  • cup almond flour
  • ¾ cup monk fruit or coconut sugar
  • ¼ cup tapioca flour
  • teaspoons baking powder
  • 1 teaspoon baking soda
  • ½ teaspoon sea salt
  • 2 eggs room temperature
  • ½ cup maple syrup
  • 1 teaspoon vanilla extract
  • 1 14-ounce can crushed pineapple, drained (see note)
  • ¾ cup pecans roughly chopped (plus more for garnish if desired)

For the cream cheese frosting

  • 1/2 cup grass-fed better room temperature sub vegan butter for dairy-free
  • 1/2 cup coconut oil room temperature
  • 1/3 cup cream cheese room temperature
  • 1 cup powdered monk fruit or use regular powdered sugar
  • 1 teaspoon vanilla extract


  • Preheat the oven to 350F. Line a muffin tin with cupcake liners.
  • In a medium bowl, mix the dairy-free milk and vinegar. Whisk and set aside.
  • In a large bowl or stand mixer, mix the brown rice flour, almond flour, monk fruit, tapioca flour, baking powder, baking soda, and salt. Stir to blend.
  • To the bowl with the milk and vinegar mixture, add the eggs, maple syrup, and vanilla extract. Whisk. Add the pineapple whisk again until everything is combined.
  • Pour the wet ingredients into the bowl with the flour mixture and beat on medium speed. Fold in the chopped pecans. Give the batter a good stir with your spatula. Let the batter rest for 20 minutes.
  • Transfer the batter to the muffin tin, filling each cup about ⅔ to the way to the top (about a heaping ¼ cup each). Bake for 20 to 25 minutes until a toothpick inserted into the center comes out clean. Allow the cupcakes to cool in the muffin tin for 10 to 15 minutes before transferring them to a wire rack to cool completely.
  • To make the frosting, combine the grass-fed butter, coconut oil, and cream cheese in a large bowl. Using a hand beater, stand mixer, or hand blender with the whisk tool, beat until fluffy, about 30 seconds. Scrape down the sides of the bowl. You can also whisk by hand if needed. Add the powdered monk fruit and vanilla extract and beat again. Give the frosting a good stir with your spatula. Frost the cupcakes immediately, or put the frosting in the refrigerator for 10 minutes for a firmer texture.


You can also use 14 ounces of fresh pineapple and process in your food processor until a crushed consistency is reached
Keyword Dairy-free optional, Gluten-free, Oil-free, Soy-free