Healthy Pineapple Muffins with Sourdough Discard
Sourdough isn’t just for bread! One of my all-time favorite ways to use sourdough starter in the summer is baking pineapple muffins.
Incorporating active sourdough starter or discard into pineapple muffins enhances flavor and texture while making them easier to digest.
Sourdough naturally contains beneficial yeast and bacteria, which break down gluten, fructans, and phytic acid, making baked goods easier to digest. This can be especially beneficial for those with gluten or FODMAP sensitivities.
Unlike traditional sourdough bread, muffins aren’t typically long-fermented, but you can ferment the batter overnight in the fridge for even better digestibility. Mix the batter, cover it, and refrigerate it overnight before portioning into a muffin tin and baking.


The Key to Fluffy, Moist Muffins: Don’t Overmix!
One of the most important muffin-making tips? Avoid overmixing the pineapple muffin batter.
When you overmix, you develop the gluten strands in the flour too much, leading to dense, chewy muffins instead of light, tender ones.
How to Mix Muffin Batter Properly:
- Add the fresh pineapple in with the dry ingredients (trust me).
- Gently fold the wet and dry ingredients together.
- Stop mixing when you see some streaks of flour. A few lumps and dry spots are ideal!
My other muffin baking tip is always to use a thin metal aluminum muffin tin with paper liners. A metal muffin tin works way better than a silicone muffin pan.


Why Fresh Pineapple Works Best in Muffins
Using fresh pineapple gives these muffins a juicy, naturally sweet burst of flavor. Frozen and canned pineapples also work great in this recipe! If using frozen pineapple, defrost and drain off any excess liquid before using. For canned pineapple, drain thoroughly before using.


Tropical Pineapple + Fruit Combo Muffins
This pineapple muffin recipe comes together in less than 10 minutes and only takes 30 minutes to bake. While I call for only pineapple in the recipe, you can totally use a mix of fruit in this recipe! Just evenly substitute half the pineapple in the recipe for a second fruit. Here are some of my favorite pineapple + other fruit combos. Let me know in the comments if you try any of these!
- Blueberry and pineapple
- Mango and pineapple
- Orange and pineapple
- Banana and pineapple
- Carrot and pineapple
- Coconut and pineapple

Things You May Need:

Storing Baked Pineapple Muffins
Storing baked pineapple muffins properly ensures they remain fresh and delicious. Here are some tips on how to store them effectively:
- Room Temperature Storage:
- Allow muffins to cool completely.
- Place them in an airtight container lined with paper towels to absorb excess moisture.
- Store at room temperature for up to 3-4 days.
- Refrigeration:
- If the weather is hot or humid, consider refrigerating the pineapple muffins.
- Wrap each muffin individually in plastic wrap to prevent drying out.
- Store in an airtight container in the fridge for up to one week.
- Freezing Muffins:
- Cool muffins completely before freezing.
- Wrap each muffin tightly in plastic wrap or aluminum foil.
- Place wrapped muffins in a freezer-safe bag or container.
- Label it with the date and freeze it for up to 3 months.
- Reheating Frozen Muffins:
- Remove the desired number of pineapple muffins from the freezer.
- Unwrap and place on a microwave-safe plate.
- Microwave on high for 20-30 seconds or until warm.
- Alternatively, preheat the oven to 350°F (175°C) and heat muffins for 10-15 minutes until warmed.

Sourdough Pineapple Muffins with Active Starter or Discard
These sourdough pineapple muffins are sweet, tart, and full of tropical flavor. Packed with juicy pineapple, this recipe offers a summery way to use up excess sourdough starter.
- Prep: 10 minutes
- Cook: 30 minutes
- Total Time: 40 minutes
Ingredients
- 2 1/4 cups all-purpose flour
- 1/3 cup sugar
- 1/2 teaspoon baking soda
- 1 teaspoon baking powder
- 1 teaspoon salt
- 1 1/2 cups pineapple, chopped
- 1/2 cup grass-fed butter, room temperature soft/melted
- 1/2 cup sourdough starter, room temperature*
- 1 teaspoon lemon extract
- 1/2 cup whole milk, room temperature
- 2 eggs, room temperature
- Extra fresh pineapple for topping
Instructions
- Preheat your oven to 350° F.
- Line a muffin tin with paper liners.
- In a medium-large mixing bowl, combine the flour, sugar, baking soda, baking powder, salt, and pineapple.
- In a separate bowl, combine the butter, sourdough starter, lemon extract, whole milk, and two eggs.
- Whisk until combined.
- Gently fold the wet ingredients into the dry ingredients until everything is just combined. Do not over-mix. The batter should be thick, and it’s okay if there are clumps.
- Spoon the batter into the muffin tins. Optional— top with more fresh pineapple chunks.
- Bake for about 30 minutes total. Rotate the pan halfway through.
- Allow cooling for about 15 minutes.
Notes
- Frozen and canned pineapples also work great in this recipe! If using frozen pineapple, defrost and drain off any excess liquid before using. For canned pineapple, drain thoroughly before using.
- Use active starter or discard from the fridge, either way it’s “discarded” into the recipe since it isn’t used for rise.