These cottage cheese pumpkin muffins are tender, perfectly moist, full of those warm fall flavor, and perfectly sweetened with a little coconut sugar. They’re made with blended oats (so naturally gluten free!) and the cottage cheese gets blended smooth with the pumpkin, giving them a little protein boost without a cottage cheese chunk in sight. They’re hearty, easy, and exactly the kind of muffin I love having tucked in the fridge or freezer for busy fall mornings.

Pumpkin chocolate chip muffins arranged on a white surface, surrounded by a bowl of pumpkin puree, a bowl of cottage cheese, scattered chocolate chips, and a beige napkin.

Apparently I need an oat flour + cottage cheese muffin for every season

Lately, it seems that I have been falling back in love with oat-based muffin recipes. And since, yes, cottage cheese is still very much having its moment (and I mean, for good reason…bonus stealthy protein is just as lovely as stealthy veggies) and, thus, the combo of oats and cottage cheese have been making it into my muffin creations as of late. After making my Blueberry Cottage Cheese Oat Muffins approximately a million times (okay, a few dozen), I started thinking that I kinda needed a fall version. An oat + cottage cheese muffin for all the seasons, perhaps? And what is more fall than pumpkin? Thus, these cottage cheese pumpkin muffins were my obvious next move.

Now, if that mouthful of a title slightly scares you with all the things I have crammed into these muffins, I want you to know that these beauties have gone through the full family-and-friends testing circuit. Neighbors. Ken and Allie. Heck, I brought one of my test batches to my parents’ house and my mom (who taught me how to cook) tried one and immediately asked when the recipe would be up on the site. The oats make them hearty (and naturally gluten-free!), but they’re still surprisingly fluffy…I don’t think anyone I’ve shared them with has guessed they’re made with oat flour. And if you’re cottage-cheese hesitant, you really don’t taste it. Pinky promise. Blending it smooth with the pumpkin, vanilla, eggs, coconut sugar, pumpkin pie spice, and cinnamon lets it just quietly do its protein-boosting thing in the background without its flavor or texture taking over.

These gluten-free cottage cheese muffins have also very quickly become one of those muffins that just…gets eaten around here. Like a lot.I’ve been grabbing one before a workout or during those “man, I’m hungry but I need to run” moments in the day, sticking them in lunch bags, or making them as meal prep so we can grab them as part of breakfast with some fruit and breakfast sausage or Canadian bacon on those chaotic weekday fall mornings. One thing I did learn while testing: use a nice thick pumpkin puree (some brands have added water and that extra moisture can make things tricky) and please please please give your batter its little rest before baking. Those oats need a minute to hydrate and soak everything up. Rush that part and you can end up with muffins that sink instead of getting that surprisingly fluffy oat-muffin texture we’re after.

Let’s make these muffins together. Just you and me…

A hand holds a blender filled with oats, baking powder, salt, and cinnamon. Surrounding bowls hold pumpkin puree, chocolate chips, vanilla extract, and flour on a white countertop.
Toss your dry ingredients into a blender.
A hand holds a spoonful of flour over a blender filled with flour. Surrounding bowls contain chocolate chips, pumpkin puree, vanilla extract, and more flour on a white surface.
Blend until a fine, flour-like texture.
A person pours flour from a blender into a glass bowl surrounded by chocolate chips, pumpkin puree, brown sugar, vanilla, and more flour on a marble countertop.
Transfer the oat flour to a bowl.
A hand pours vanilla extract into a blender containing eggs, wet ingredients, and creamy cottage cheese for pumpkin muffins, with a bowl of flour, chocolate chips, and cracked eggshells visible on a marble countertop.
Blend all remaining ingredients (minus the chocolate chips).
A person pours a blended wet mixture into a bowl of dry ingredients on a marble counter, preparing to make cottage cheese pumpkin muffins. Chocolate chips and a muffin tin with paper liners are nearby.
Pour the blended mixture into the bowl of dry ingredients.
A person stirs chocolate chips into a bowl of yellow batter with a black spatula, preparing delicious cottage cheese pumpkin muffins. Cupcake liners and a white dish with more chocolate chips are nearby on a marble countertop.
Add in the chocolate chips.
A person stirs cottage cheese pumpkin muffin batter in a glass bowl with a spatula. Cupcake liners are arranged in a baking tray nearby on a marble countertop.
Give everything a stir then let rest for 15 minutes.
A person uses an ice cream scoop to fill muffin liners with batter for cottage cheese pumpkin muffins in a muffin tin. A bowl of batter and chocolate chips are nearby on a white countertop.
Evenly divide the batter among your prepared muffin tin cups.
A person places chocolate chips on cottage cheese pumpkin muffin batter in a 12-cup muffin tin lined with paper liners. A small bowl of chocolate chips sits nearby on a marble surface.
Sprinkle a few extra chocolate chip on top, if you like.
A person holds a muffin tin filled with freshly baked cottage cheese pumpkin muffins, with one muffin being lifted out. A bowl of chocolate chips and a cooling rack are nearby.
Pop them in the oven and bake until golden and set. Let cool then enjoy.
A hand holds a cottage cheese pumpkin muffin with chocolate chips, broken in half to reveal the moist, orange interior. Other muffins and a bowl of pumpkin puree are visible in the blurred background.
Pumpkin chocolate chip muffins arranged on a white surface, surrounded by a bowl of pumpkin puree, a bowl of cottage cheese, scattered chocolate chips, and a beige napkin.
5 from 12 votes

Oat Cottage Cheese Pumpkin Muffins

Yield: 12 muffins
Prep Time: 10 minutes
Cook Time: 18 minutes
Total Time: 28 minutes
Cuisine: American
Course: Breakfast
These cottage cheese pumpkin muffins are tender, perfectly moist, full of those warm fall flavor, and perfectly sweetened with a little coconut sugar. They’re made with blended oats (so naturally gluten free!) and the cottage cheese gets blended smooth with the pumpkin, giving them a little protein boost without a cottage cheese chunk in sight. They’re hearty, easy, and exactly the kind of muffin I love having tucked in the fridge or freezer for busy fall mornings.

Ingredients
 

  • 2¼ cups (220 g) uncooked rolled oats, Use certified gluten-free if needed
  • 1½ teaspoons pumpkin pie spice
  • 1 teaspoon cinnamon
  • 1 teaspoon baking powder
  • ½ teaspoon baking soda
  • ¼ teaspoon salt
  • 3 large eggs
  • ¼ cup (59.15 ml) avocado oil
  • 1 cup (230 g) low-fat cottage cheese
  • ¾ cup (240 g) canned pumpkin puree, I found thicker brands, like Libby, worked best.
  • ½ cup (77 g) coconut sugar, or unpacked light brown sugar
  • 2 teaspoons (8 g) vanilla
  • 1 teaspoon apple cider vinegar
  • ⅓ cup mini chocolate chips

Instructions
 

  •  Heat the oven to 375℉. Line 12 compartments of a standard muffin tin with paper liners or grease with oil spray.
  • Since this muffin recipe uses less added oil than most traditional muffin recipes, I find that silicone liners or disposable liners with a natural food-grade silicone coating (I like If You Care baking cup liners) work best to prevent sticking. If using traditional paper liners without a coating, lightly spray them with cooking spray before filling so the muffins release more easily after cooling
  • Add the oats, pumpkin spice, cinnamon, baking powder, baking soda and salt to your blender. Blend until the mixture looks like flour, about 30 seconds. Pour the oat flour into a large bowl and set aside.
  • Add the eggs, cottage cheese, pumpkin puree, oil, coconut sugar, vanilla and vinegar to a blender. Blend until all the ingredients are combined and very smooth.
  •  Pour the contents of the blender into the mixing bowl with the oat flour mixture. Add the chocolate chips to the bowl too.
  • Stir until the dry ingredients are just incorporated into the batter. Careful not to over mix! Let the batter rest for at least 15 minutes so that the oat flour can soak up the moisture. This helps the texture of the muffin and prevents muffins from sinking.
  • Use a heaping 1/4 cup measuring cup or scoop to divide the batter into the 12 prepared muffin cups and top each one with a few more chocolate chips, if you’d like.
  •  Bake until the tops are lightly golden brown and the muffins have an internal temperature of 200℉, about 16-18 minutes.
  •  Allow muffins to cool completely then enjoy or store in an airtight container at room temperature for a day then refrigerate for 4 to 5 days. Muffins can be individually wrapped then frozen for up to 2 months.

Notes

Recipe Testing Notes from Taesha
  • If you already have oat flour, you can replace the blended oats with 220g of oat flour. Just make sure they are certified gluten free if these being celiac-safe is needed.
  • I have made these with full-fat cottage cheese and they work great, but I don’t recommend using fat-free. In my testing, there is too much water in fat-free and it results in the muffins sinking. 
  • I have tested this recipe with maple syrup and honey and found that it added too much moisture to the batter and the muffins had a wet texture, so I don’t suggest swapping out the granulated dry sweetener with a liquid one in this recipe. 
Serving: 1muffin, Calories: 185kcal, Carbohydrates: 22g, Protein: 6g, Fat: 8g, Saturated Fat: 2g, Polyunsaturated Fat: 1g, Monounsaturated Fat: 4g, Trans Fat: 0.01g, Cholesterol: 48mg, Sodium: 242mg, Potassium: 124mg, Fiber: 2g, Sugar: 9g, Vitamin A: 2471IU, Vitamin C: 1mg, Calcium: 59mg, Iron: 1mg
Nutritional information provided here is only an estimate shared for convenience and as a courtesy. Information will vary based on ingredients + brands used to create the recipe.