Healthy Butternut Squash Brownies with Cottage Cheese

These healthy butternut squash brownies are fudgy, chocolaty, and secretly nourishing thanks to butternut squash puree and protein-packed cottage cheese! Whether you’re baking them up for a weeknight treat or surprising your family with a healthier dessert option any night of the week, these gluten-free brownies check every box: rich flavor, better-for-you ingredients, and that classic brownie satisfaction.

Healthy Butternut Squash Brownies with Cottage Cheese

These brownies are so easy because everything comes together in the blender with simple, everyday ingredients. There’s no fancy prep or complicated steps – just blend, pour, and bake!

The blended cottage cheese and butternut squash do all the work to keep the brownies moist and fudgy, without extra effort.

It’s the kind of recipe you can throw together quickly and still end up with bakery-worthy brownies. Happy baking!

Why you’ll love these wholesome butternut squash brownies

Fudgy yet wholesome – With squash and cottage cheese, these brownies strike the perfect balance of indulgence while also being a nutritious dessert. They’re real brownies, with extra goodness added into them.

Gluten-free & protein-rich – Almond flour and cottage cheese make these a smart choice for fueling your body while still enjoying dessert. They are higher in protein than your average brownie and made with wholesome ingredients.

Kid-approved hidden vegetable – A sneaky way to get in some extra veggies (your kids will have no idea they’re in there).

Simple ingredients you’ll need for butternut brownies

Scroll down to view the recipe card below for the full ingredients list, nutrition facts, and step-by-step instructions.

• Eggs – For structure and richness.
• Butternut squash puree (canned or homemade) – The star of the show! Adds natural sweetness and moisture.
• Cottage cheese – Blended in for protein and creaminess (you won’t taste it!).
• Vanilla extract – For a warm, sweet aroma.
• Almond flour – Keeps the brownies gluten-free while adding a nutty undertone.
• Natural cane sugar – Just enough sweetness without going overboard.
• Unsweetened cocoa powder – For that deep chocolate flavor.
• Baking powder – Helps the brownies rise slightly.
• Sea salt – Balances and enhances the chocolate flavor.
• Dark chocolate chips – Melty pockets of chocolate goodness.

How to make healthy butternut squash fudge brownies

Step 1: Preheat the oven to 350 degrees F. Line an 8″x8″ baking pan with parchment paper for easy removal.

Step 2: Add everything except the chocolate chips to a blender or food processor and blend until the batter is a smooth texture. Stir in the chocolate chips into the batter.

Step 3: Pour the blended butternut squash mixture into your prepared pan and bake for 30 minutes for fudgy brownies or 38 minutes for a cakier texture.  Let the brownies cool for at least 15 minutes before slicing. Optionally, drizzle pieces of brownies with melted chocolate and sprinkle with flaky sea salt.

Watch me make easy brownie recipe

The full how to video can be watched below, or on my YouTube channel!

Pro tips

• Don’t overbake – Pull them out at the fudgy stage (around 30 minutes) if you love gooey fudgy texture.
• Cool before slicing – This helps the brownies set and slice cleanly.
• Blend well – A smooth batter ensures the cottage cheese and squash disappear into the background and no one notices it.

How to store leftovers

• Room Temperature: Store in an airtight container for up to 2 days.
• Fridge: Keeps well for 5-6 days, and they get even fudgier as they chill.
• Freezer: Wrap slices individually and freeze for up to 4 months.

Serving ideas

These delicious brownies are amazing on their own, but you can also:

• Add a dollop of Greek yogurt or whipped cream on top.
• Drizzle with warm peanut butter or almond butter.
• Pair with fresh berries for a chocolate-fruit combo.

Substitutions, optional variations & dietary adjustments

Below you’ll find a list of substitutions that will work well in this healthy brownies recipe. 

If you try something different out, please leave a comment below letting us all know how it turned out!

Eggs – If you need an egg-free option, try using 2 flax eggs (2 tablespoons ground flaxseed mixed with 5 tablespoons water, rested for 5 minutes). The brownies will be slightly more fudgy and less structured, but still delicious.

Butternut Squash Purée -You can swap in pumpkin puree or sweet potato purée in equal amounts. Both offer similar moisture and natural sweetness, though pumpkin has a slightly more earthy flavor, while sweet potato leans sweeter.

Cottage Cheese – Not a cottage cheese fan? Plain Greek yogurt or ricotta cheese works well as a 1:1 replacement. For the best texture, blend until smooth before adding to the batter.

Vanilla Extract – Vanilla paste or vanilla bean powder can be used in place of extract. If using paste, swap 1 teaspoon of paste for 2 teaspoons of extract.

Almond Flour – Oat flour is a great substitute and keeps these gluten-free brownies soft and tender. Add 1-2 tsp of melted coconut oil or avocado oil if you opt for oat flour, since it’s lower in fat compared to almond flour. You can also use cashew flour, pecan flour, or any nut flour. Coconut flour is not recommended here unless you significantly reduce the amount and increase moisture.

Natural Cane Sugar – Pure maple syrup or honey can be used instead (¼ cup), though the brownies may be slightly softer. For a lower-sugar option, coconut sugar works as a direct swap.

Cocoa Powder – Dutch-processed cocoa powder can replace regular cocoa powder for a richer, smoother chocolate flavor. Just note the brownies may be slightly darker in color. Raw cacao powder works here too!

Dark Chocolate Chips – Milk chocolate chips, chopped chocolate, or dairy-free chocolate chips all work. You can also omit them for a less sweet brownie or replace them with chopped walnuts or pecans for a crunchy texture.

More healthy dessert recipes you’ll love

• 3 ingredient banana brownies
• Pumpkin chickpea blondies
• Vegan black bean brownies

If you try this healthy butternut squash brownies recipe, I’d love it if you left a star rating and comment below letting me know how it turned out!

XO

Heather