These soft, bakery-style lemon raspberry sourdough muffins are made with sourdough discard, fresh lemon zest, and juicy raspberries, creating a tender crumb and bright, fresh flavor in every bite.

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There is something comforting about pulling a tray of homemade muffins from the oven. These lemon raspberry sourdough muffins are one of my favorite ways to use up sourdough discard while creating something truly special for the family.

If you’ve been looking for the perfect sourdough discard muffin recipe, this one checks every box. It’s bright yet cozy, simple yet bakery-worthy. You can bake them the same day, or allow the batter to long ferment overnight for improved digestion and add depth of flavor.

Let’s bake.

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Why You’ll Love These Lemon Raspberry Sourdough Muffins

Simple and easy to throw together.

These lemon raspberry sourdough muffins use simple, whole food ingredients making them easy to throw together in a pinch. 

Bakery-style

The bright flavors of lemon and raspberry, tender crumb, and beautiful golden domes make these muffins taste like they are fresh from the bakery. 

Sourdough Recipe

Sourdough recipes have probiotics which are beneficial for gut health and making baked goods more digestible. 

The sourdough flavor also adds a nice touch to baked goods.

Food prep

These muffins freeze very well as fully baked muffins or as muffin batter.

Freeze for up to 3 months in an airtight container or freeze the batter in a disposable freezer bag for fresh muffins at a later date. 

Flexibility

These lemon raspberry sourdough muffins are flexible. 

Because you can use active starter or sourdough discard in this recipe, you can bake them immediately if you would like to without waiting for a rise time. The extra fermentation time is optional though may benefit those who have a hard time with digesting gluten.

Lemon raspberry sourdough muffins are perfect for an after school snack, slow Saturday mornings, spring brunch, or served with afternoon tea.

Why Sourdough Discard?

If you keep a sourdough starter, you know the rhythm of feeding and discarding. Instead of tossing that discard, baking with it is one of the simplest ways to reduce food waste and stretch your ingredients further.

To get started with sourdough, you can find my incredibly simple, step-by-step guide here: How to Make a Sourdough Starter from Scratch- Easy Guide

Using sourdough discard in muffins:

• Adds a subtle tangy depth of flavor
• Improves texture and tenderness
• Reduces food waste
• Can improve digestibility when long fermented

When you allow the batter to rest overnight in the refrigerator, the natural fermentation process begins breaking down some of the grains before baking. If you’re sensitive to gluten, this long-fermented sourdough muffin method may make them easier to tolerate.

It’s a simple shift that turns an ordinary muffin into something more nourishing and flavorful.

Tools You’ll Need for Lemon Raspberry Sourdough Muffins

Large mixing bowl or bowl of a stand mixer

Hand mixer or stand mixer paddle attachment 

Medium bowl

Citrus press

Standard sized large muffin tin

Muffin liners or parchment paper to make liners with – I love using tulip liners for a special look but any regular muffin liners will work. 

Muffin scoop– 2oz. scoop, ice cream scooper, or spoon for scooping batter

Measuring cups and spoons

Plastic wrap, beeswax wrap, tea towel or bowl cover

Ingredients You’ll Need

For the Muffins

• 2 cups all-purpose flour (246g) + 2 tablespoons flour for coating berries (For gluten sensitivity, use rice flour since this flour used to coat the berries will not be long fermented)
• 1 tablespoon double-acting baking powder
• 1/2 teaspoon salt
• 1/2 cup butter, melted (112g) I always opt for salted but unsalted will work- I recommend increasing the salt by 1/8 teaspoon if using unsalted butter
• 1 cup granulated sugar (231g)
• 2 large eggs, room temperature
• 1/2 cup sourdough starter/discard (133g)
• 1/2 cup sour cream (125g)
• 2 tablespoons fresh lemon juice (juice from 1 medium-sized lemon)
• 1 tablespoon lemon zest (zest from 1 lemon)
• 1 1/2 cups raspberries (fresh or frozen) I prefer frozen because they are more difficult to smash when mixing

For the Streusel Topping

• 1/2 cup all-purpose flour (110g)
• 1/4 cup granulated sugar (58g)
• 4 tablespoons cold butter (56g)
• Zest of 1 lemon (optional but recommended)

These ingredients come together to create bakery style sourdough muffins with a bright citrus finish and tender crumb.

How to Make Lemon Raspberry Sourdough Muffins

Melt butter & Cream with sugar

Melt the butter and allow it to cool slightly. You don’t want it hot when mixing or it may scramble the eggs.

Cream the melted butter and sugar together until smooth and well combined. The mixture should look glossy and slightly thickened.

Add the Wet Ingredients

To the butter and sugar mixture, add:

• Sour cream
• Lemon juice
• Lemon zest
• Sourdough discard

Stir gently until incorporated.

Add the eggs one at a time, mixing just until combined after each addition. Avoid overmixing — we want tender muffins, not tough ones.

Mix the Dry Ingredients

In a separate bowl:

• Spoon and level the flour (do not scoop directly with the measuring cup, this will result in denser muffins since scooping results in more flour. I recommend weighing your ingredients with a food scale for optimal results)
• Add salt
• If baking immediately, add baking powder.

If you plan to long ferment the batter overnight, omit the baking powder for now. We will add it just before baking.

Combine

Fold the dry ingredients into the wet ingredients gently. Stir only until no dry streaks remain. The batter will be thick.

Cover the bowl with an airtight lid, damp tea towel, or reusable bowl cover.

At this point, you may proceed with baking — or choose the long fermentation option below.

Long Fermentation Option (Overnight)

If you would like to make long fermented sourdough muffins, place the covered bowl in the refrigerator overnight.

The next morning:

• Remove the bowl from the refrigerator
• Allow it to sit at room temperature for 20–30 minutes

This resting period helps take the chill off before adding the remaining ingredients.

Adding the Baking Powder and Raspberries

If you omitted the baking powder the night before, sprinkle it evenly over the batter now and gently fold to evenly incorporate throughout the batter.

Place the raspberries in a small bowl. Sprinkle with 2 tablespoons flour (or rice flour if gluten sensitive). Gently toss to coat. This light coating helps suspend the berries in the batter and prevents excess moisture from sinking the muffins.

Carefully fold in the raspberries using a wooden spoon or spatula. Work slowly to avoid crushing them.

Streusel Topping Instructions

In a small bowl:

• Combine flour and sugar
• Cut in cold butter using a pastry cutter or your fingers until crumbly
• Stir in lemon zest if using

The mixture should resemble coarse crumbs. Do not overwork it — small lumps of butter create the best texture.

This lemon raspberry streusel muffin topping adds both sweetness and a slight texture that contrasts beautifully with the soft crumb.

Bakery-style Domes

This is where the magic happens.

1. Preheat your oven to 425°F.
2. Let the oven sit at temperature for a full 20 minutes before baking.

That resting time ensures the oven has truly reached temperature which is important to activate the baking powder essential the muffin tops to rise and create beautiful bakery domes.

Line your muffin tin and fill each liner about 3/4 full. Top each muffin generously with 1–2 tablespoons of streusel.

Bake:

• 425°F for 8 minutes
• Without opening the oven, reduce heat to 350°F
• Continue baking for 18–22 minutes

Do not open the oven for at least the first 10–15 minutes. That initial high heat burst rapidly activates the baking powder, creating steam and lift. This is the simple trick to achieve those tall, bakery-style domes.

Check for Doneness

Insert a cake tester or toothpick into the center of the largest muffin. If it comes out clean or with a few moist crumbs (not wet batter), they’re ready.

Allow the muffins to cool completely in the pan set on a wire rack. This prevents soggy bottoms, sinking domes and helps the structure set properly.

Enjoy!

Storage & Freezing

Counter: 1–3 days in an airtight container
Refrigerator: Up to 5 days
Freezer (baked muffins or unbaked batter): Up to 3 months

To freeze baked muffins, allow them to cool completely. Wrap individually or store in an air-tight container.

Freezer Batter Hack (My Favorite Meal Prep Tip)

This is one of my favorite make-ahead tricks.

After mixing the batter, transfer it into a gallon-sized (disposable) zip-top bag. Freeze flat.

When ready to bake:

• Thaw overnight in the refrigerator
• Snip the corner
• Pipe into muffin liners
• Bake as directed

This method makes fresh baked lemon raspberry sourdough muffins possible even on busy mornings. I prefer this method over freezing individually to save space and maintain that fresh from the bakery style muffin.

Baker’s Schedule

Same-Day Bake (About 1 hour total)

8am Preheat oven and mix up batter
8:15am Fold berries and fill liners
8:20am Bake 8 minutes at 425°F
8:28am Reduce to 350°F
8:50am Remove from the oven to a wire rack and cool

Overnight Long Ferment Schedule

Evening (10 minutes active time)
Mix batter (omit baking powder). Cover and refrigerate.

Morning
7:45am Remove batter from the fridge and preheat oven to 425
8:15am Mix in baking powder, fold in berries and fill liners
8:20am Bake 8 minutes at 425°F
8:28am Reduce to 350°F
8:50am Remove from the oven to a wire rack and cool

Troubleshooting Guide

Even simple recipes can have small hiccups. Here’s how to fix them.

Muffins sank in the middle?

• One muffin may have had too many berries.
• They may have needed a few more minutes baking.

Dense texture?

• The batter may have been overmixed.
• Baking powder may be expired.

Too wet?

• Frozen berries were not coated in flour.

Flat tops instead of domes?

• Oven was not fully preheated.
• Oven door opened too early.

These small adjustments make all the difference.

More Sourdough Discard Recipes

• Double Chocolate Sourdough Muffins
• Sourdough Gingerbread Muffins
• Sourdough Discard Maple Scones
• Sourdough Vanilla Bean Scones