Whenever there's more than one focaccia flavour I want on the table and only enough space in the oven for one pan to bake it in, this is the recipe that solves it. Sourdough Focaccia Muffins are the same overnight dough I've been using across this site for years, just divided into a muffin tin instead of committed to a single tray, so three completely different toppings (or 12!) come out of one batch. Nobody has to agree on a flavour. Everybody gets their own.
Jump to:
- Recipe Highlights
- Ingredient Notes
- Mix and Match: How to Bake Three Focaccia Flavours in One Muffin Tin
- How to Make Sourdough Focaccia Muffins
- Tips for Great Sourdough Focaccia Muffins
- Troubleshooting Sourdough Focaccia Muffins
- Recipe FAQs
- Serving Suggestions
- Storage and Make-Ahead
- More Sourdough Flavours
- Sourdough Focaccia Muffins
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If we haven't met before, hi, I'm Ieva, and I test every sourdough recipe on this site from my kitchen in North Wales. This one started as a way to stop arguing about toppings and turned into genuinely my favourite way to bake focaccia when I want more than one thing.
Recipe Highlights
TASTE: oil-rich base on every one, three completely different toppings (or you can personalise all 12!)
ONE BATCH, THREE FLAVOURS: jalapeño cheddar, rosemary and sea salt, olive and herb are in this batch
THE TIP: If you want to experiment with higher hydration dough, this is the best recipe for it. I went up to 310g of water in this recipe, and it was messy to shape but gorgeous once baked!
SEB'S RATING: Loves variety because it makes him feel like a judge on a cooking show. No actual scores given, but all the flavours sampled and no complaints filed.
Ingredient Notes
- Strong bread flour, 12%+ protein. Same logic as every other sourdough focaccia on this site: enough gluten structure to hold a wet dough together without it collapsing.
- Active sourdough starter, 100% hydration. Fed and doubled before you start the dough.
- Olive oil, in the dough. Worked in by hand once the fermentolyse rest is done, not the mixer. More on why in the method below.
- Olive oil, for the muffin tin. This is the one doing something genuinely different to a normal greased tray. You want a proper pool in the base of each hole, not a light brushing round the sides. That pool is what shallow-fries the base of every focaccia as it bakes, and it's the whole reason you get a crisp, almost-fried edge instead of a pale one.
Find the full ingredient quantities and instructions in the recipe card below.
Mix and Match: How to Bake Three Focaccia Flavours in One Muffin Tin
This is the actual reason to make sourdough focaccia muffins instead of a tray bake: you can commit different groups of holes to different toppings, from one batch of dough, in one bake. No mixing three separate doughs, no committing an entire tray to a flavour half the table won't eat.
For the batch pictured, I divided the dough into twelve and topped four the way I do my Jalapeño Cheddar Sourdough Focaccia, four the way I do my Simple Rosemary Sourdough Focaccia With Sea Salt and four the way I do my Overnight Sourdough Focaccia Bread with Olives.
Follow whichever linked recipe matches the topping you're after, but only use its topping method, on only the holes you've set aside for it. The base dough and bake below cover the rest.
It doesn't stop at those three. Anything from my 12+ Sourdough Focaccia Bread Recipes & Topping Ideas roundup will work the same way. Pick three, pick one, pick six or 12 if you're going all out. The point is you're no longer locked into a single flavour just because that's what fits in a tray.
And you can even go for half savoury, half sweet as long as your savoury toppings aren't super pungent, because... you know, nobody wants a garlic-infused Cinnamon Apple Sourdough Focaccia muffin.
How to Make Sourdough Focaccia Muffins
Day 1: dough and bulk fermentation
1. Feed your starter first thing in the morning and leave it somewhere warm until it's at least doubled. I feed mine in a 1:1:1 ratio (starter:water:flour), and it usually doubles, sometimes triples, within four hours.
2. In the bowl of a stand mixer, combine the flour, water and active starter. Mix on low for a few minutes until the flour is hydrated, then cover the bowl and leave it to fermentolyse for an hour.
3. Scatter over the salt and drizzle in the oil for the dough, then work both in by hand. Don't be tempted to just run the mixer for this bit - the dough will split, separated by oil layers instead of coming together.
4. Once it's incorporated, mix on medium for 10-12 minutes until smooth and elastic. It'll still be wet, but it should start gathering round the hook rather than sitting in a puddle at the bottom of the bowl.
5. Scoop the dough into a lightly oiled bowl, cover, and leave somewhere warm (21-24°C) for 30 minutes. Over the next three hours, at 30-minute intervals, give it six sets of coil folds using wet hands.
6. Let bulk fermentation finish undisturbed for another 1.5-3 hours, depending on how warm your kitchen is. You're looking for a 50-60% rise, visible bubbles under the surface, and a soft, jiggly texture when you nudge the bowl. Then it goes straight in the fridge for 8-24 hours, or simply overnight.
Day 2: dividing, topping and baking
1. Generously oil each hole of your muffin tin using the 2-3 tablespoons reserved for the tin. This is the step that's genuinely different from any tray focaccia I've written up, so don't rush it: you want a visible pool sitting in the base of each hole, not a quick wipe of oil round the sides.
2. Tip the dough out onto a lightly floured surface and divide it into 12 pieces, roughly 70-75g each. Shape each piece into a loose, taut round and drop it into an oiled hole.
3. Cover the tin loosely and leave it somewhere warm to proof for 1-12 hours, until each portion has puffed up and domed above the rim of the tin.
4. Preheat the oven to 200°C (400°F). Oil your fingers and dimple each focaccia individually, right down to the base, then top according to your mix-and-match plan, working topping by topping across whichever holes you've assigned to it.
5. Bake for 15-18 minutes, until deep golden brown and crisp at the edges. Individual portions bake faster than a full tray, so start checking at the 15-minute mark rather than assuming your usual focaccia time. Ovens vary, and you know yours better than I do.
6. Leave the focaccias in the tin for 5-10 minutes before carefully turning them out onto a wire rack. Let them cool a few minutes more before eating. They're best served slightly warm.
Tips for Great Sourdough Focaccia Muffins
🫒 Don't skimp on the oil in the tin. A proper pool, not a brush of oil, is what makes the base crisp rather than pale and slightly steamed.
⚖️ Weigh your dough before dividing if you want an even bake. A few grams' difference between portions is enough for some to finish before others.
🎨 Commit toppings to groups of holes, not the whole tin. Doing more than one flavour is far easier to portion and serve if each topping has its own clearly defined block of holes rather than being scattered around.
🔥 Check at the early end of the bake time. Smaller portions colour faster than a full tray does, and a couple of minutes too long is the difference between crisp and dry.
🧊 These freeze well individually. Genuinely useful if twelve is more than you'll get through in two days, and it means you always have a few different flavours on hand rather than a full tray of one thing.
Troubleshooting Sourdough Focaccia Muffins
Base came out pale instead of crisp. Almost always down to too little oil in the tin before the dough went in. A quick brush round the sides isn't enough, you need an actual pool sitting in the base of each hole. If you're confident the oil was generous enough, check your oven with a separate oven thermometer. An oven running cooler than it claims will bake the dough through without properly colouring or crisping the base.
Some portions finished baking before others. This comes down to dividing the dough by eye rather than by weight. A difference of even 5-10g between portions is enough for the smaller ones to catch colour and dry out while the larger ones are still pale. Weigh each piece on a kitchen scale if you want a properly even bake across all twelve.
Dough stuck to the tin. Usually means the oil pool wasn't generous enough, or the focaccias didn't get their full 5-10 minutes to rest in the tin before you tried to turn them out. Both the oil and that short rest are what let them release cleanly. Use a high-quality muffin pan - we love our USA Pan Muffin Tin and would highly recommend it.
Toppings burned before the base finished baking. More likely with anything delicate, like thinly sliced garlic or fresh herb leaves, sitting right at the edge of a portion. Tuck delicate toppings more towards the centre of each dimple, where they're less exposed to direct heat from the tin's edge.
Recipe FAQs
Roughly 70-75g per hole for a standard 12-hole muffin tin, which is one batch of this dough divided evenly into twelve. Weigh the pieces if you want an even bake, since a few grams' difference between portions is enough for some to finish baking before others.
Yes, this is the same dough used across my other sourdough focaccia recipes, just scaled (x1.5) and shaped differently. Use a lightly oiled 9x13in tray instead of a muffin tin, and expect a longer bake, closer to 20-22 minutes, since a full tray takes longer to cook through and colour than individual portions.
Serving Suggestions
Good for a table where everyone wants something different, and a solid bread basket alternative if you're feeding a crowd for dinner. Best served slightly warm, ideally within an hour or two of baking, while the base is still at its crispest.
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Storage and Make-Ahead
Keep them in an airtight container at room temperature for up to 2 days. To freeze, wrap them individually once fully cooled and store for up to 2 months, then reheat from frozen in a hot oven for about 10 minutes to bring the crisp base back.
More Sourdough Flavours
If mix-and-match has you thinking past these three toppings, my 12+ Sourdough Focaccia Bread Recipes & Topping Ideas roundup is the full list to pick from, and this post will get added there once it's live. For building your own flavour combinations from scratch rather than following one of mine, my Flavoured Sourdough: How, When and What Mix-Ins To Add guide covers the ratios and timing for adding your own mix-ins without throwing off the dough.
Sourdough Focaccia Muffins
Ingredients
- 390 g strong bread flour with at least 12% protein content
- 285 ml water
- 165 g active sourdough starter 100% hydration
- 8 g salt
- 35 ml olive oil for the dough, + 2-3 tablespoon extra for the muffin pan
- see notes for topping suggestions
Instructions
DAY 1:
- First thing in the morning, feed your sourdough starter and leave it in a warm spot to at least double in volume. We typically feed our starter in a ratio of 1 part starter: 1 part water: 1 part flour, and it doubles (or even triples) within 4 hours.
Fermentolyse and Mixing The Dough
- In the bowl of a stand mixer, combine the flour, water and active sourdough starter. Mix on low speed for a few minutes, until the flour is hydrated. Cover the bowl with a damp tea towel and leave the dough to fermentolyse for an hour.
- After an hour, scatter the salt over the dough and drizzle in the 35ml olive oil. Using your hands, squish the salt and oil into the dough, aiming to distribute both evenly. Don't be tempted to just mix the oil in by running the stand mixer - the dough will split, separated by oil layers.
- Once incorporated, run your mixer on medium speed for 10-12 minutes, until you have a very smooth and elastic dough. It will be wet, but it should start gathering around the dough hook.
Coil Folds, Bulk Fermentation, Cold Proof
- Scoop the dough into a lightly oiled bowl. Cover with a damp tea towel or cling film and leave in a warm place (21-24°C) for 30 minutes.
- Over the next 3 hours, at 30-minute intervals, perform a set of coil folds using wet hands - six sets in total.
- Cover the dough and let it finish its bulk fermentation undisturbed for 1.5-3 hours, depending on the temperature of your kitchen. You're looking for a 50-60% rise, visible bubbles, and a soft, jiggly texture.
- Place the dough in the refrigerator for 8-24 hours (or simply overnight).
DAY 2:
Dividing and Second Proof
- Generously oil each hole of your muffin pan using the reserved 2-3 tablespoons of olive oil - you want a proper pool in the base of each one, not just a light coating. This is what gives the base of each focaccia that crisp, almost-fried edge.
- Tip the dough out onto a lightly oiled surface and divide it into 12 equal(ish) pieces (roughly 70-75g each). Use oiled hands to shape each piece into a loose round and drop it into an oiled muffin hole.
- Cover loosely with large bag (make sure the top doesn;t touch the dough) or an inverted large roasting tray and leave it in a warm spot to proof for 1-1.5 hours, until each portion has puffed up and domed nicely above the rim of the tin.
Topping and Baking
- Preheat the oven to 200°C (400°F).
- Oil your fingers and dimple the top of each focaccia all the way down to the base, the same way you would with a full tray.
- Top each one with whatever you please - see Notes below for what I used, but this is very much a mix-and-match bake.
- Bake for 15-18 minutes, until deep golden brown on top and crisp at the edges. Individual portions bake faster than a full tray, so start checking at 15 minutes rather than assuming the full time - ovens vary and you know yours better than I do.
- Leave the focaccias in the tin for 5-10 minutes before carefully turning them out onto a wire rack. Cool for a few more minutes before eating - they're best served slightly warm.
Video
Notes
Nutrition
Elena says
What a great idea to make sourdough focaccia muffins! So much fun for a party and so many ways to do the toppings. Delicious!
Ieva Greber says
Thanks, Elena — they really are made for playing around with toppings, and perfect for a party spread. Glad they went down well!