Cooking with ferments
Heat kills what's alive but leaves the flavor. When to use a ferment raw, when to add it at the end and when to put it in the pan, ferment by ferment.
7 min read First steps Reviewed October 26, 2026 23 facts, each with its source
Heat and what's alive
A homemade ferment is full of live microbes, and strong heat kills them. The high temperatures of canning kill lactic acid bacteria1, and baking kills every bacterium in sourdough2. So there are two ways to cook with ferments, and both work:
- Raw or at the end, with the heat off. The ferment reaches the plate alive and keeps its sourness and crunch.
- Cooked. It loses what's alive, but the flavor stays, and that's what you want in a stew or a loaf.
Choose according to the dish. What makes no sense is boiling a ferment and expecting it to stay alive.
The brine
Don't pour it out. The brine from pickles or sauerkraut is sour and salty, and it works in dressings, as a marinade in the fridge or as a splash in a cold soup or a stew once it's served. Mind its salt: a 5% brine holds 50 g per liter3, so taste the dish before you salt it.
Only use brine from a batch that went well. If a jar has mold, all of it goes, brine included4. Whatever you take out of the jar goes in the fridge and gets used soon: Clemson gives used pickling liquid a day or two for a sauce, a dressing or a marinade5, and Fervida applies the same to brine.
Sauerkraut and kimchi in the pan
Sauerkraut takes heat well. Sautéed with onion, in a stew with potatoes and sausages or in a hot sandwich with cheese, it changes little: even frozen and later heated, it barely loses texture6.
For cooking, the best kimchi is the ripest. By day five to seven it's tangier and softer7, and that's the one for fried rice, scrambled eggs or a stew with tofu. Young, crunchy kimchi is best raw.
Miso
Miso is a live ferment: that's why it sometimes swells its packaging8. Its flavor comes from koji enzymes, which break down proteins and give umami9. In a soup, turn off the heat, loosen the miso in a bowl with a little broth and add it at the end, without letting it boil again: that way it keeps its aroma. It also works in dressings, as a glaze for eggplant or fish in the oven and rubbed on vegetables before roasting. There the heat takes what's alive and leaves the flavor.
Shio koji
Shio koji is a seasoning of rice digested under high salt10: one study measured it at about 11% salt11. Use it instead of salt, not on top of it.
Its enzymes break down protein: three times as much as ginger and an eighth as much as kiwi12. That's why it tenderizes meat and fish. Those enzymes hold up for half an hour at 50 °C (122 °F) and weaken with more heat13: the marinade works cold and cooking stops it.
Always marinate raw meat and fish in the fridge14. If you want to use the marinade as a sauce afterward, boil it first15.
Kefir, yogurt and labneh
Kefir is for drinking, goes into smoothies and stands in for buttermilk, yogurt or sour cream in recipes16. In a cold sauce or a dressing it arrives alive; in a cake or pancakes it brings acid and liquid, and the oven takes care of the rest. Yogurt and labneh work the same way: cold in sauces, dressings and spreads; in a stew, at the end and over low heat, so they don't curdle.
Sourdough discard
What's left over when you feed your starter can be shared, frozen, used in other recipes or composted17. What you don't do is eat it raw: tasting raw dough can give you food poisoning18, because germs in flour die only when it's baked or cooked19. Pancakes, crackers or batter, always cooked through.
Preserved lemons, hot sauces and crème fraîche
With preserved lemons, it's mostly the peel you use. Scoop out the pulp, rinse the peel if you want it less salty20 and chop it fine into a chicken stew, a couscous or a dressing. A fermented hot sauce takes heat like any sauce, but its sourness comes through more if you add it at the end. Crème fraîche, with all its fat, can boil without curdling: it's the one for a hot sauce where yogurt wouldn't hold.
Over-fermented kombucha and homemade vinegar
A kombucha that has fermented too long tastes like vinegar, because its bacteria turn the alcohol into acetic acid21. Use it as a mild vinegar in dressings, never for pickling: its acidity isn't known either. The same goes for homemade vinegar: save it for salads22 and don't use it for pickling, because its acidity is unknown23.
When each one goes in
| Ferment | When | For example |
|---|---|---|
| Brine | Raw | A dressing, a cold soup |
| Sauerkraut | Raw or cooked | A salad; a stew with sausages |
| Kimchi | Young, raw; ripe, cooked | As a side; in fried rice |
| Miso | At the end, not boiled | A soup; a glaze in the oven |
| Shio koji | Before cooking, in the fridge | A chicken or fish marinade |
| Kefir, yogurt and labneh | Raw or at the end | A cold sauce; a cake |
| Sourdough discard | Always cooked | Pancakes, crackers |
Where every number comes from
Every number in the text leads to its figure: the exact sentence from the official guide it comes from, in its own language.
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1
The high heat of canning kills lactic acid bacteria
“However, the high temperatures of canning will kill any beneficial Lactobacillus bacteria.”
University of Minnesota Extension · Preserving food at home: Fermentation (reviewed 2026) · read on October 25, 2026
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2
Baking kills every bacterium in sourdough
“The baking step will kill any bacteria present.”
Colorado State University Extension (Farm to Table) · Sourdough Starter Best Practices (March 2020) · read on October 25, 2026
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3
A 5% brine holds 50 g of salt per liter
“5% 50 g / L liquid”
UC Master Food Preservers, Inyo-Mono · Brine Math Made Easy · read on October 20, 2026
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4
If there's mold, the whole batch goes
“If you confirm mold growth on any part of a ferment, it should be immediately discarded.”
UC Davis, Department of Food Science and Technology · Common issues with fermented fruits and vegetables (v1.0, 15-mar-2022) · read on October 20, 2026
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5
Used liquid, in the fridge and within a day or two
“If the pickling solution has been used, it can be stored in the refrigerator and reused in a day or two for barbecue sauce, coleslaw dressing or a marinade.”
Clemson Cooperative Extension, Home & Garden Information Center · Common Pickle Problems (HGIC 3101, revised August 2020) · read on October 26, 2026
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6
Sauerkraut frozen and later heated barely changes texture
“freezing and thawing sauerkraut that is later heated would not cause a noticeable change in texture”
University of Minnesota Extension · Preserving food at home: Fermentation (reviewed 2026) · read on October 25, 2026
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7
By days 5 to 7, kimchi is tangier and softer
“By days 5 to 7, the kimchi develops a tangier flavor, a more pronounced aroma, and a softer texture.”
University of Georgia Cooperative Extension · Homemade Kimchi: A Science-Based Guide to Safe Fermentation (Circular 1362, 2025) · read on October 20, 2026
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8
Miso is alive: that's why it sometimes swells its packaging
“As products are live, continuing fermentation may be the underlying reason for a recall of bulging packaging.”
BC Centre for Disease Control, Environmental Health Services · Safety of Fermented Foods, Section 3.10: Koji foods: miso, soy sauce and amazake (September 2023, updated December 2024) · read on October 25, 2026
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9
Koji enzymes break down proteins and give umami
“proteases break down proteins into amino acids and peptides, providing the savory umami taste”
BC Centre for Disease Control, Environmental Health Services · Safety of Fermented Foods, Section 3.10: Koji foods: miso, soy sauce and amazake (September 2023, updated December 2024) · read on October 25, 2026
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10
Shio koji is a seasoning of rice digested under high salt
“Shio-koji is a gruel-like fermented rice seasoning that is obtained from the digestion of rice under high-salt conditions.”
日本食品科学工学会誌 (Maehashi K., Ohto A., Yamamoto T., Asari M., Kashiwagi Y.) · 塩麹製造での熟成温度が残存酵素活性に及ぼす影響 (Effect of Temperature on Enzymatic Stability in Shio-Koji During the Maturation Process, 2015) · read on October 25, 2026
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11
One study measured shio koji at about 11% salt
“maintained at about 11％ during the entire storage period.”
日本調理科学会誌 (Enguchi N., Yukawa N., Nakanishi Y.) · 自家製塩麹のカゼイン分解活性 (Caseinolytic Activity of Homemade Shio-Koji, 2016) · read on October 25, 2026
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12
It breaks down protein three times as much as ginger and an eighth as much as kiwi
“The caseinolytic activity of shio-koji was three times that of ginger and about 1/8 of the activity exhibited by kiwi-fruit.”
日本調理科学会誌 (Enguchi N., Yukawa N., Nakanishi Y.) · 自家製塩麹のカゼイン分解活性 (Caseinolytic Activity of Homemade Shio-Koji, 2016) · read on October 25, 2026
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13
Its enzymes hold up for 30 minutes at 50 °C (122 °F) and weaken with more heat
“The caseinolytic activity of undiluted shio-koji did not change after 30 minutes at 50℃, but its activity declined at higher temperatures.”
日本調理科学会誌 (Enguchi N., Yukawa N., Nakanishi Y.) · 自家製塩麹のカゼイン分解活性 (Caseinolytic Activity of Homemade Shio-Koji, 2016) · read on October 25, 2026
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14
Always marinate raw meat in the fridge
“Always marinate raw meat in the refrigerator.”
University of Illinois Extension · Meat Safety: Marinating · read on October 26, 2026
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15
A marinade that touched raw meat is boiled before it's used as a sauce
“bring the marinade to a boil, which will kill harmful bacteria.”
University of Illinois Extension · Meat Safety: Marinating · read on October 26, 2026
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16
Kefir stands in for buttermilk, yogurt or sour cream in recipes
“It can be enjoyed as a refreshing drink, added to smoothies, or used in recipes as a replacement for buttermilk, yogurt, or sour cream.”
Colorado State University Extension (FoodSmart Colorado) · Understanding and Making Kefir · read on October 20, 2026
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17
Discard can be shared, frozen, used in other recipes or composted
“If there is more removed starter than needed, excess starter can be shared, frozen, used in other recipes, composted, or discarded.”
Colorado State University Extension (FoodSmart Colorado) · Sourdough Basics: Caring for your Starter and Making Bread (reviewed October 2025) · read on October 25, 2026
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18
Tasting raw dough can give you food poisoning
“Tasting or eating raw (unbaked) dough or batter can put you at risk for food poisoning.”
CDC · Raw Flour and Dough · read on October 25, 2026
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19
Germs in flour die only when it's baked or cooked
“Germs are killed only when flour is baked or cooked.”
CDC · Raw Flour and Dough · read on October 25, 2026
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20
Rinsing takes away some of the salty flavor
“rinse to remove the salty flavor”
Clemson Cooperative Extension, Home & Garden Information Center · Common Pickle Problems (HGIC 3101, revised August 2020) · read on October 26, 2026
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21
Kombucha bacteria turn the alcohol into vinegar
“In the second step, the bacteria in the SCOBY ferments the alcohol to produce vinegar (acetic acid).”
Virginia Cooperative Extension (Virginia Tech) · What do I need to know to sell KOMBUCHA at the farmers market? (FST-297, last reviewed November 2025) · read on October 20, 2026
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22
Save homemade vinegar for salads
“Save the homemade or flavored vinegars for things like salads.”
Clemson Cooperative Extension, Home & Garden Information Center · Common Pickle Problems (HGIC 3101, revised August 2020) · read on October 26, 2026
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23
Homemade vinegar's acidity is unknown: it's not for pickling
“The acidity level of homemade vinegars is unknown and may make the pickles unsafe.”
Clemson Cooperative Extension, Home & Garden Information Center · Common Pickle Problems (HGIC 3101, revised August 2020) · read on October 26, 2026