"What Did I do Wrong???" (The Definitive Homemade Yogurt Troubleshooting Guide)

This post may contain affiliate links, including Amazon.com. Your price won't change but it enables free content & supports our family business.

Anytime you’re growing something, there’s always some problem that could go wrong.

Whether your goal is to grow a child, a vegetable garden, a goldfish or, you know, bacteria, living organisms are by nature dynamic. Sometimes they die. Sometimes they get sick. Sometimes they grow faster, or slower or…chunkier.

If you’ve made an odd batch of homemade yogurt, this is the “help line” to call!

runny yogurt troubleshooting

Help, My Yogurt Turned Out…

  • Chunky
  • Cottage-cheesy
  • Runny
  • Lumpy
  • Separated into whey plus thick cheesy weird stuff!

Honestly, for all these texture/consistency problems, you need to troubleshoot in the same way. Your problem might be:

  • Temperature
    • Be sure to incubate your yogurt only between 90-110F – over 116 or so kills the bacteria completely, but over 110 tends to hinder them and you get runny or cottage cheesy yogurt. I’ve found that about 100F makes the best thickness.
    • A problem – you might start at the right temp, but if your pot of water is too hot, it can raise the temp of the cooler WAY too high. I learned that an electric stove, for some reason, holds the heat in the pot more. My yogurt at my in-laws was terrible for weeks! I finally figured out that I couldn’t boil it right before putting the jars in the cooler. I had to put the pot in the cooler while the jars were cooling and/or allow some “cool down” time to let the steam out. You might use an oven thermometer with a wire that comes out of the cooler so you can check the temp while the lid is closed, since opening the lid will alter the environment.
    • Another problem – be aware of summer vs. winter temps. I learned I can’t get the cooler out of the way in the garage in the summer unless I take precautions and use warm, not boiling, water. It just got too toasty in there! On the other hand, you might be able to incubate without a cooler if you have a steamy garage at about 95F.
    • If you have a problem over and over with texture and think it may be inconsistent incubation temps, you might try regulating it with a dehydrator just to see what happens – I’ve had good luck with my Excalibur dehydrator with all the trays out at 105F.
  • Amount of starter
    • Too little starter makes runny yogurt, but too much (more than 2 Tbs./quart for pasteurized or 2 1/2-3 Tbs. for raw yogurt) makes things separate into whey and thick cheese. Renee of MadeOn lotion says to spread that cheese on bread and broil, and your “oops” tastes like good mozzarella. Smile
  • Quality of starter
    • If you’ve been using the same yogurt to restart your new batches, sometimes it just starts to wear out. I used to buy a new starter every  month or two, then I got better at consistency and could go 6 months. Sometimes if you get frustrated with the thickness of your yogurt, it’s worth spending a few bucks to start over, or try a powdered starter from your local health foods store, Cultures for Health, or order via Amazonthis one is popular and I’ve heard this one is very good too.
    • If you  haven’t made yogurt in a while, your starter is probably weak. I wouldn’t bother using yogurt that is over a month old, and less than 2 weeks is optimal.
  • Kind of milk
    • If using raw milk, fresher is better. It’s tempting to make yogurt with milk that’s about to turn, but you’ll probably get a funky consistency. Best to pasteurize and then make yogurt.
    • Skim milk (and other reduced fat milks) will always make considerably thinner yogurt. Read about the benefits of full fat dairy first, and if you still insist on using skim, try the gelatin trick here.
  • How you finish
    • Don’t stir or shake your jars after incubating and before cooling. Just let them be.
    • Try putting a jar in the freezer for an hour after incubating vs. just in the fridge. One reader even found that if she let the jars sit on the counter for 2 hours after incubating, she had a wonderfully creamy batch!

Raw milk yogurt notes: Keep in mind that the natural healthy bacteria in raw milk will compete with the yogurt cultures, and raw yogurt is notoriously less thick than pasteurized. Get tips on making raw milk yogurt at this week’s earlier post.

Five “Runny Yogurt” Fixes

homemade yogurt troubleshooting

1. You can follow the directions to fix runny yogurt with gelatin if you consistently have runny problems. That fix will not help if you already have runny yogurt in the fridge, though, as the gelatin needs to be added when the milk is warm.

2. If you keep your milk hot between 160-180F for 20-30 minutes, according to this helpful post at Cultures for Health, it will break down the milk proteins so they will coagulate better. This really works, but again, won’t help if your yogurt is already runny.

3. Strain it like yogurt cheese – follow the directions in this post but instead of letting it drain all the way to a cream cheese consistency, just stop after 30-60 minutes for a thicker yogurt.

4. Make green smoothies with it.

5. Bake with it, such as pancakes (yogurt usually takes the place of milk just fine) or this soaked baked oatmeal recipe.

Help, My Yogurt is Too Sour!

Longer incubation times typically make for more sour yogurt, but so do higher temperatures. Four hours is sufficient to make yogurt. Experiment with 4, 6, or 8 hours to see what you like. For a while, 6 hours was too tangy for me, but now I love it at 12-16 hours, so don’t be afraid to leave one jar fermenting after you take the others out to see what you think. Add boiling water to keep the temp up after 8-12 hours.

Help, I Broke a Jar!

I’m sorry for your loss.

No really, I am. I hate breaking jars. It happened to me twice this month, so even the yogurt lady guru breaks jars. It keeps me humble. I can’t always pinpoint exactly what went wrong, but here are a few things to check:

  • Is your washcloth covering the entire bottom of your pot?
  • Are you using high quality jars? Quart jars rated for canning usually do better (but not 100%) than reused store jars.
  • Don’t lid your jars while you’re heating them up.
  • Don’t let your pot boil like crazy. That’s never a good thing. Winking smile Set your timer so you don’t burn the house down.
  • Start with cold water surrounding the jars instead of hot water.
  • If you’re using water in the sink to cool the jars, make sure you put the jars in the empty sink, then add cool water slowly up to half the jar, then add some ice, and cringe. If you’re in that much of a hurry, know that you’re running the risk of jar breakage.

Even if you lose a quart of milk, remind yourself how darn much money you’re saving making homemade yogurt – more than a quart of milk over time!

Help, My Yogurt Smells Like…

…dirt, grass, rotten food…

Uh, yeah. If it smells like anything other than fermented milk (which isn’t incredibly pleasant for everyone, but you should recognize the aroma), trust your nose. Throw it out and start over. You may have grown some extra bacteria on accident (or it’s too old). Be sure to use clean jars and clean hands and utensils.

Troubleshooting Yourself

One of the great beauties of the jar-in-pot method is that you can do different things in the same batch – different kinds of milk, different temperatures or amount of starter. If you’ve got a consistent issue, write down a few fixes and try them on different jars. For example:

  • stir in 2, 3 and 4 Tbs. starter into different jars
  • start the process at 95F, 100F, 105F and 110F in various jars
  • do some raw and some pasteurized
  • pull jars at 4, 8, 12 and 16 hours incubation
  • incubate in two different places
  • store in three different places after incubating – fridge, freezer, countertop

Keep track of your results on paper – it will be worth it to be a little academic about it for a week or two, because once you nail it, hopefully it’s like riding a bike from then on and you won’t even have to think about it.

Need more help?

Remember that there’s an online forum to “ask the teacher” in the Cultured Dairy & Cheese eCourse, where you can see a video of me making homemade yogurt using the jar-in-pot method. For some folks, seeing it in person has made all the difference in building confidence, much like my water kefir video got a lot of people starter with that process.

More FAQs

  • Can I make dairy-free yogurt?
    • Try this method with almond milk that a reader found, and you can use coconut milk with this jar-in-pot method and a bit of gelatin to thicken. A few more thoughts on that here.
  • What about that crockpot method?
    • It’s not for me because of the pain of washing that insert…but if you want to try it, many love it! Click for the option to make crock pot yogurt.
  • Is there a less complicated way?
  • How do you eat this yogurt?
  • What kind of milk should I use?
    • That question is answered near the bottom of this post, including info on UHT organic milk.
  • I’m still scared!
  • I strained my yogurt. What do I do with whey?
  • How long will my yogurt keep?
    • At least a month is safe; beyond that, use your nose. Cultured products last longer than fresh milk.
  • Can I freeze homemade yogurt?
    • Freezing yogurt is FINE as far as keeping the bacteria alive. You can even freeze yogurt in 1 Tbs. portions and use it as a starter for another batch, but sometimes it will be slightly weaker than a brand new, fresh starter.
    • The issue with freezing yogurt for eating is its thawed consistency. Once thawed, frozen yogurt separates and is runny, so if you want it for smoothies or just don’t mind a weird consistency, you’ll still get your probiotics, but don’t expect thick, creamy yogurt once you freeze it.

Quick Notes

Just wanted to let you know that there’s a pretty big sale on NaturoKits through this Sunday, over $10 off! If you’ve been interested in trying natural health but don’t know where to start, this first aid kit is for you. Shop here.

Also, “the Berkey Guy” has his new LPC Survival website up, and it’s fantastic. As a longtime KS sponsor, I’m happy to highlight his business – you’ll want to check it out if you’re interested in filtering your water or real food preparedness.

Now you’d better be off to the kitchen to make some yogurt! Think of me while you’re enjoying it….Mmmmmm…

Pin It

Disclosure: I am an affiliate of Amazon, Cultures for Health, and GNOWFGLINS. See my full disclosure statement here.

Click here for my disclaimer and advertising disclosure - affiliate links in this post will earn commission based on sales, but it doesn't change your price.

53 Bites of Conversation So Far

  1. Rebecca says

    A nice comprehensive yogurt troubleshoot page! :-)

    I’ve hit the riding-the-bike phase. I’ve finally figured out what works for us and it comes out consistently thick every time. Yay!

  2. says

    I agonize over any yogurt that I mess up. I just stew over it all day…and then dream about it at night. My main problem? I get in a hurry and add the starter at the wrong time.

    • Katie Kimball @ Kitchen Stewardship says

      Ah, yes, a good way to practice patience…I’ve been victim of the “hurry up” runny yogurt too! 😉 Katie

  3. says

    What a killer guide! Thanks so much for all the work you put into this. My yogurt is almost always on the runny side and almost always ends up in smoothies and baked goods. I’ve got some gelatin in the cupboard and plan on giving that a whirl next time I get a runny batch.

    • Mechef145 says

      Wow! Did you try preparing in an un-glazed clay pot? I regularly prepare healthy, delicious & thick yogurt at home in just 3 easy steps. You need milk, live culture and this clay pot (yogurt pot) and I am sure you will have no problem doing the same right in you kitchen. Here is the link that will guide you step by step “http://miriamsearthencookware.com/how-to-make-thick-delicious-yogurt/”

  4. Katherine says

    I find that starting with cold water reduces breakage. I think hot water with cold milk stresses the glass.

  5. says

    I have to mention that I found if I stir or disturb the freshly cultured, warm yogurt in any way, that will ruin my texture and cause the curds and the whey to separate. I am very careful to remove the jars, put the lids on, and move them immediately to the fridge without stirring or disturbing. I let them chill completely before touching them. This has made a difference.

    Still need to make yogurt…but don’t have any fresh milk. Tomorrow….

  6. Amanda says

    Thanks for being so thorough, and for all your stuff in general. I wish your way worked for me, because the no-dishes thing is just wonderful. Mostly, I don’t have pot(s) big enough to put enough jars in to make yogurt in the quantities that works for me, and I find that heating the yogurt in the jars makes for a lot of scrubbing when they’re empty.

    So, not to deflect readers (because, Katie, obviously, you’re awesome!), but if anyone else needs to try a different method, I’ve had good luck with the method Kristen at The Frugal Girl uses (http://www.thefrugalgirl.com/2009/10/how-to-make-homemade-yogurt-2/). It’s fussier (I don’t sterilize though), but I find it’s worth it…I’ve gotten consistently thick yogurt, with no real risk of jar breakage.

  7. Megara says

    Hi Jenny, Can you use the whey from coconut milk yogurt? If so for what? can you use it to ferment vegetables?Ketchup,potatoes sauerkraut etc ? Thank you Megara

    • Katie Kimball @ Kitchen Stewardship says

      I’ve really never experimented with coconut milk yogurt, so sorry! If it’s cultured properly, it should be able to be used for all those purposes, but I would check with a fermentation master like GNOWFGLINS.com or the book Wild Fermentation. :) Katie

  8. says

    Glad you included about setting the timer when you make it. I forgot I had started a batch of yogurt last week and fell asleep and awoke to the smell of something burning! There was no fire, thank the Lord, but it was a good reminder to set the timer!

  9. Katie says

    Hi – I just tried making yogurt for the first time and unfortunately, I ended up with a pot of whey with a giant cheese curd separated into the middle of the pot. Just wanted to share that I strained some of the whey and they added eggs, sugar, cinnamon, vanilla to make a crustless “yogurt-cheese cake.” It turned out pretty delicious, so if you are wondering what to do with your yogurt fail, that’s one suggestion.

  10. Melissa says

    Hi there! I have made some great batches of yogurt with your awesome instructions! I have a question about buying a starter. For some reason I’m having a hard time finding a small cup of plain non fat yogurt. Can I use plan non fat Greek yogurt as a starter? I tried today and it didnt come out and sorta smelled funny but I’m hoping my mistake was rushing or not checking the temp (today was not the day to make yogurt but I did it anyway) . If I am forced to buy a large tub of plain yogurt can I freeze it in small batches to use for starter?

    Thanks again for your time!

    • Katie Kimball @ Kitchen Stewardship says

      Yes to both! Yogurt freezes fine and retains the live bacteria; I recommend freezing in 1 Tbs. portions for easy yogurt-making.

      Also, Greek yogurt often makes great yogurt. :) Any plain (or even sweetened, I hear) yogurt will work. Enjoy! :) Katie

  11. jen says

    I just made yogurt (cultured overnight in the oven with pilot light) but forgot to take it out the next morning. It was “culturing” for about 41 hours before I remembered it. It smells and tastes fine. Nice and tangy. Do you think it’s still okay to eat? Thanks!

    • Katie Kimball @ Kitchen Stewardship says

      If it was at the right temp for that long, I’d feel better about it. I can’t say I’ve ever let it go more than 24 hours though! Trust your nose…

      :) Katie

  12. Lynne says

    Tried to make yogurt for the first time – used grass fed whole milk and three different types of starters in the various jars. I just went to check it after four hours and it is still like milk. Thoughts?

    • says

      There are so many factors, but basically if it is still totally liquid and no yogurt smell, you probably got the temp too high and killed things, or radically too low and nothing could propagate. I hope you figure it out for next time! :) Katie

    • Katie Kimball @ Kitchen Stewardship says

      Fizzy as in little bubbles, like carbonation? I’ve never had that happen. Maybe you over-whisked the starter in? Ultimately, if it still smells like yogurt, you had some fermentation happening. If it acts liquid like milk, you can either start over with boiling it or just use it in baking. Sorry I took so long to find your comment; it came in just before my book launch and I was absolutely swamped.
      :) Katie

      • Sonia says

        My last batch of yogurt is fizzy now too, but it wasn’t at first. This hadn’t ever happened to me before and have been making it for over 2yrs. It still tastes fine.. just carbonated. I’m not sure if I could still use it for my next batch, but will err on the side of caution and just get a new starter.

        • janine says

          I’ve been making yogurt for about 2 years and just had my first part of a batch go fizzy. I think it stayed in the fridge a bit too long. It’s almost like it’s fermenting like an apple cider would. Gross but not harmful, I’m guessing.

  13. Kaitlyn says

    When I heated my raw milk on the stove top (to pasteurize it myself to 180) it got very chunky. Is this normal? I’m currently cooling it to 90-110.

    • Katie Kimball @ Kitchen Stewardship says

      I’m wayyyy too late to help, but I’ve only seen that happen when there’s already yogurt in it…so if you just had raw milk, I’m guessing it was starting to “clabber” either from being at room temp too long or being old. ??? Katie

  14. Brie says

    I made my first batch of yogurt and didn’t realize I shouldn’t stir it before it set. It completely separated. Can I use The thick part that is left for anything?

  15. audrey says

    I tried checking to see if this question was already asked. i made yogurt twice and it came out runny… i set the temp in the oven so chances are either i stirred in the starter too hard and/or didn’t add enough. My question is… if it didn’t turn out (it’s pretty much still milk), can I use that same batch and just do it all over again?

    • Kaitlyn says

      Same thing has happened to me. Didn’t seem to ferment at all and looked liked milk at the end of the process. I chose to throw it away since I couldn’t be sure that the right kinds of bacteria were still there. Better safe than sorry?

    • Katie Kimball @ Kitchen Stewardship says

      I’ve had this happen before, but usually if it truly still looks like milk, you started too hot or it got too hot and didn’t culture at all because the bacteria were killed. Stirring too hard won’t cause this problem. Because there’s a little bit of yogurt in there, reheating it usually causes some weird separation and it’s not a great base for new yogurt. I just use it on cereal OR better, cook with it, like a creamy soup or rice pudding. Then you can make sure you boil it to set your mind at ease about bacteria. Good luck next time! :) Katie

  16. Michelle says

    I am making cream cheese for the 1st time from raw milk I left it out for two days coverd with a lid in a mason jar. It’s about 70-75 degrees in my house. I got a cream cheese thin layer on top but the rest is like thin water. Was it to cool in my house? Is that liguid whey, if so can I use it as whey? or is it bad?

    Thank you!

  17. candice says

    So I tried to make my first batch of raw milk yogurt today in the crockpot and it got too hot and has separated into whey and thick cheesy stuff, is it still usable?

    • says

      Obviously I’m wayyyy too late to be of any help for you, but I’ll answer for others searching this thread:
      If it smells like yogurt or milk, you’re fine to use it in other ways. Bake with the whey, put it in smoothies, etc. Sorry I got so behind on comments and yours got buried! Hope you’ll try again – Katie

  18. Janice says

    Using a timed yogurt maker, the time ran out and the yogurt sat for approx 2 hrs before I realized what had happened. I needed it to cook for an additional 5 hours (SCD ) so I restarted the yogurt maker. Is that a problem?

  19. CK says

    I just wanted to share for anyone else with this problem: I completely over-cultured a huge batch of yogurt last week and ended up with curds on the bottom and clear yellow whey on top. I strained all the whey out with cheesecloth and the remaining curds/paneer substituted nicely for ricotta in my stuffed manicotti recipe. So you don’t have to dump it all out if this happens to you!

  20. raisue says

    Help–I forgot to cool milk before pouring it into my starter (before putting in oven). Is it still worth it? I’m giving it a try…but wondering what will happen.

  21. Max Planck says

    I came across this article google-ing something FroYo related. I thought I’d just pass along how I make yogurt which is pretty problem proof. I measure out the amount of milk I need by almost filling my quart thermos. Then I heat my milk to 175 in a pot, cool it to 115, and pour everything but a tablespoon or so into the thermos. I stir in (Greek) yogurt. Pour the milk in the thermos back into the pot (to mix). Pour into the thermos. Cap, shake, and let sit till the next day (12-24 hrs). Always comes out good. NB- shaking seems to make it creamier as does the Greek yogurt. Less tart at 12 hrs. Shake before emptying usually is easier.

  22. Zoe says

    So this morning I made a batch of yogurt (I use a yogurt maker). However, I just now realized that I forgot to add the starter to the milk after heating it and cooling it (I just put it in the machine, turned it on, and went on with my day like normal).

    The finished product still looks like yogurt. It set up just fine, like my other batches. What is it? It doesn’t smell bad. It doesn’t smell like yogurt either. Any ideas? I’m not going to consume it, cuz it freaks me out a little. I would think that warm milk without any starter in a yogurt machine would just stay warm milk. Any ideas??

    • Lisa says

      You still had bacteria in the milk, just not necessarily the “chosen” cultures. You were really lucky in the bacteria who chose to come live in your batch.

      I culture my yogurt for 24 hours to banish lactose and break down the casein. Any tips on how to cut the tangy taste? Less time is not an option.

    • says

      Hi Saadia,
      If you mean gummy like sticky or stringy, both could be the temperature and duration of incubation. It’s just something to test for yourself and figure out the magic numbers for your yogurt starter! If it smells good, it’s still good to eat or use in smoothies. :) Katie

  23. Linda says

    I dehydrated yogurt in dehydrator for the usual 24 hrs last night but forgot to take it out. Put it in fridge this morning after an extra 8 hrs. @ room temp. It looks fine. What do ya think? (I made 4 qts!)


  24. Samantha says

    Help, I forgot to put my freshly made yogurt (in a yogurt maker) in the refrigerator. It sat at room temperature for 12 hours. It smells fine but is a little watery. Is it ok to eat? Thanks!

Take a Bite (of conversation)

Your email address will not be published. Required fields are marked *