Why did my tomatoes separate in the jar?


If you have seen separation in your home canned tomatoes, you may be wondering just what causes this to happen. Heating the product before putting it in the jar; otherwise known as a hot pack can help prevent this separation.

Separation in canned tomato products is not unsafe. It merely reflects the action of enzymes in tomatoes that have been cut and allowed to sit at room temperature. The enzymes that naturally occur will begin to break down pectin in the tomatoes.  This breakdown results in a yellow red tinted liquid that can appear in either the top or bottom of the jar.  In tomato juices, a quick shake of the jar will make the layer disappear.  The layers will reappear after the contents of the jar resettle.  In canned whole tomatoes, the separation cannot be dispersed by shaking the jar.  You can safely use both the tomato layer and the liquid layer while making other foods like spaghetti sauce or chili but it is a bit unappealing in the jar.

Be sure to follow the directions for the hot pack carefully as overheating the tomatoes can also cause separation of the solids and liquids. Our favorite recipe for canning tomatoes is from the National Center for Home Food Preservation.

Enjoy the rest of tomato season!



Liz Meimann

I received both my undergraduate and graduate degrees in Food Science at Iowa State University. I love to quilt, sew, cook, and bake. I spent many years gardening, canning, and preserving food for my family when my children were at home.

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49 thoughts on “Why did my tomatoes separate in the jar?

  1. I sometimes cold pack, and add hot liquid, while other times hot pack my tomatoes. I have separation either way. I use a pressure canner and process for 10 minutes at 11 PSI (often higher as it’s hard to control on electric stove).

    My husband and I are wondering if the tomatoes are in the pressure can way too long (from start to finish), and are over processed. Is this a possibility?

  2. I think you may be right about the tomatoes being over processed. If your PSI exceeds 11 pounds then that would be the cause of the over processing rather than the duration of time they are in the canner. Better control over the PSI would yield better quality tomatoes.

  3. I just cold packed diced/smushed tomatoes in a cold water bath canner. They separated and the next day I shook the jars because the pulp was stuck to the top of the jar and looked kind of dry. This brought the liquid and pulp back together but also I saw lots of bubbles in the jar. The bubbles dissappated after a couple hours.
    Still, I am unclear if the tomatoes are ok?
    Thank you for your input!

  4. Hi, as long as you followed a safe, tested recipe, the separation in the tomatoes is not a problem. This separation occurs when there is some time between the first cutting of a tomato and the processing of the tomatoes. Enzymes in the tomatoes work to separate the pulp from the juice and you will see a clear layer of liquid (tinted orange) and then the solids floating in the jar. Shake them before use. If you wish to avoid this issue, when you are preparing tomatoes for processing, begin heating them on the stove after you have peeled the first couple of tomatoes. Put a pan on low heat and as you peel more tomatoes, add them to the pot. This stops the enzymatic activity which leads to separation.

  5. I am getting separation in my canned salsa.
    As I make the salsa, the peppers are roasted but the tomatoes are just boiled to peal.
    Both peppers and tomatoes are pulse blended in a food processor.
    When mixed together they get more than a tsp of salt.
    The salsa is at room temperature when put into jars.
    Lids are coming out of hot water bath and put on finger tight.
    I have processed pints in boiling water for 35 min and goth both separation and boil over in jars.
    I have processed 12 oz. jars for 25 min and got both separation and some boil over in jars.
    What am I doing wrong???
    Ingredients are Roma tomatoes, 3 kinds of peppers, very small amount of garlic and onion (both fresh) and sea salt.
    Welcome any advice 🙂

  6. Hi David, the separation is due to enzymatic action inside the tomatoes after the tomatoes have been cut and before they have been heated enough to kill the enzymes. So, for the entire time after peeling until the salsa is cooked inside the canner, the enzymes are at work. This enzymatic action causes the separation of the tomatoes after canning. If you heat the tomatoes from the time they are peeled, you can eliminate the separation. Please feel free to call us for further discussion.

  7. I very often process mixed batches of home grown veggies. So, I might have green beans, corn, tomatoes, squash — in separate jars. When I do that, I always pressure can the entire batch for the lowest acid/highest pressure/time requirement food. I do not, in this case, add acid to the tomatoes, because they always require the least amount of time/pressure. I’m essentially over processing, I think. These are tomatoes that end up in sauces or soups. My real question is about whether over processing makes them unsafe in any way?

  8. Hi, the over processing will not make them unsafe, however, the tomato processing time is assuming the acidification of the tomatoes so you may not actually be over processing them. I do not know and can not guess or estimate what a safe time would be for unacidified tomatoes.

  9. I pressure can mine. My instructions say process for 25 minutes with 10 pounds of pressure.
    Seems like a long time to me. What do you think?

  10. Why is there a difference in processing time on pressure canned tomatoes between cold pack with added water vs. cold pack tomatoes only?. I add water, but a very small amount to fill each jar and process at 11psi for 10 minutes. Two tablespoons lemon juice per qt.

  11. After I took my crushed tomatoes out of the bath and sat it on the counter, I heard a pop in the lid. Is that normal? First time doing this.

  12. Michael, I don’t have the food science background to explain why there is a difference other than to say it has to be in the way heat transfer takes place inside the specific product jar to reach the safe temperature. Extensive studies have been done to determine the amount of time and/or pressure needed to process foods safely. No matter how you choose to can your tomatoes, all steps in preparing and cooking the foods need to be followed for the process time/pressure given for the specific product being canned along with acidification (which you mention) to insure absolute food safety. The National Center for Home Food Preservation is a great resource.

  13. Stacy, DEFINITELY! Pat yourself on the back and hope that you hear a pop from each jar removed from the canner. The pop is the sound of success telling you that the lid has closed tightly over the jars and that they are properly sealed. The pop takes place when the flat lid sucks into place during the cooling process.

  14. Question, I haven’t made my mother’s recipe for tomato preserves in a long time. But my brother begged me to can some for him. I followed the recipe closely, at the end it instructed me to remove the pan from the burner and stir in the liquid Certo then put in prepared jars. I did. Why didn’t the preserves thicken? What could I have done wrong?

  15. Karen, without seeing your recipe, I am going to make an educated guess at what went wrong. In your narrative you say that you removed the pan from the burner, stirred in the Certo, and then jared the preserves. In order for Certo to jel properly, it needs to be boiled for 1 minute before the preserves are jared. Here is a link to directions for remaking: https://extension.oregonstate.edu/sites/default/files/documents/8836/sp50604remakingsoftjellies.pdf. Also, if you are using an old recipe, you will want to process the preserves in a hot water bath. Since the 1980s the USDA has made this recommendation for preserves of all types intended for shelf use. You will see in the Oregon State directions for remaking, 5 min of processing time. If altitude is above 1000 ft, it should be 10 min.

  16. I canned some tomatoes and understand there may be some separation. They have all sealed properly. Several of the jars have an inch or so of space from top with no liquid or tomatoes. Question being: Is it ok that there is that much airspace in the finished product? Second question: Is there a way to attach a picture for you to see exactly what I am looking at?

  17. Eric, What has happened is called siphoning. That’s when some of the liquid leaks out during processing. It’s very common and many struggle with it. It can be caused by under-tightening of the rings, failing to get all of the air bubbles out of a jar before putting the lid on, having the temperature fluctuate during canning or cooling the jars too rapidly. If your jars seal and you have more than half of the liquid remaining, they will still be shelf stable. The food sticking out above the liquid line might turn a little darker color, but it doesn’t effect the flavor and is not dangerous in any way. Use jars with the least liquid or most headspace ahead of those that are closer to the appropriate headspace.
    In regard to your second question, you can email your question with picture attached to answer@iastate.edu.

  18. I’ve been canning for years following my mother’s steps since I helped her as a child. She always wrapped the cooked jars in towels and left them overnight. Of course I’ve always done this too and wonder if you’ve heard if this and why it’s done. Thanks!

  19. Donna, I am not sure what you mean by wrapping the cooked jars in towels. If you mean jars processed in a hot water bath or steam canner, then please discontinue to the practice. Researchers at the University of Wisconsin-Madison have found that the natural cooldown process is important to the sterilization of the product. Therefore, it is important to follow the proper cool down process after water bathing or steam canner processing, for both the safety and quality of your home canned products. Here is the cool down procedure: When the water bath processing / steam canning time is up, turn off the heat, and remove the canner lid; Leave the jars as they are in the canner; Set a timer for 5 minutes; At the end of 5 minutes, remove the jars and place them on a towel or a wire rack somewhere away from cold drafts; Do not cover jars; do not touch rings; Let jars sit untouched for 12 to 24 hours. Don’t cover the jars in an attempt to lengthen the time that the jars stay warm — you run the risk of your jars developing flat sour or jeopardizing the safety of the product. Bacteria inside the jar are still being killed while the jars are cooling down from the high heat of the boiling water. The wrapping of the towel holds the product in the unsafe zone for too long. For researched based recipes and the most up-to-date canning methods, please check out the National Center for Home Food Preservation and the 2020 USDA Complete Guide to Home Canning. Canning is a science and much has changed since our mother’s canning time.

  20. Thank you so much for your quick and thorough response! So I’ve followed my mothers process (As you’ve described) for over 30 years. But—you definitely spell out the scientific rationale and it’s hard to argue With that! Thanks. I’ll follow your advice . Very helpful!

  21. How do I prevent tomato juice from separating? I saved the juice from straining tomatoes for salsa, brought it to a boil, and processed pints in a water bath for 35 minutes.

  22. Sarah, as the blog post Why did my tomatoes separate in the jar? says, separation is the dirty work of enzymes in the tomatoes. Actually it is thought to be caused by the enzyme, Pectose (Pectinesterarse), found in high concentrations in tomatoes. The enzyme is activated when tomatoes are cut. To reduce separation, heat tomatoes quickly over high heat to 82 C (180 F) to destroy the enzyme. Pectose is the reason that some prefer to not crush tomatoes outright but rather crush them after heating tomato quarters as they are cut. The gradual preparation method allows heating to occur relatively rapidly to kill the enzyme off before it gets a chance to act. Crushing or pulverizing follows the cooking. Besides the enzyme having time to act, by using the run-off juice from the tomatoes, you don’t have much of the solid left.

  23. It was my 1st time making Tomato juice and the question was about the separation and the orange liquid was it ok or could It be dangerous to use after it set..all lids popped by old way ..woot woot .I was just thinking could this cause or be salmonella..so whewww..Thank you for answering this question for so many of us

  24. Help….1st time trying pressure canning raw pack tomatoes and when I opened the canner, saw that the ring and lid were off one of the jars…..tomatoes everywhere. However, the glass did not shatter Any thoughts on what happened?? Txs much! I have a dial gauge canner so processed at 11 pounds psi for 25 minutes.

  25. Lettie, I can so relate to your experience; last year I had the same thing happen while canning tomatoes. For me it was three jars and oh what a mess inside the canner! I heard popping noises shortly after I turned the canner off. It was the first, and I hope the last, time for such to happen in all of my nearly 50 years of canning. After searching many resources for the cause, the only suggestion I found is that the rings/bands were either tightened too much or too little. While it is common for the rings/bands to loosen slightly during processing, they should not come off. You want the ring to be just tight enough to keep the lid in place and loose enough to allow air in the jar to escape or vent. Headspace is also critical in the venting process. Obviously there is air in the headspace as well as between pieces of food, in the canning liquid, and inside the pieces of food. The jar needs to vent this out during processing because oxygen can cause spoilage. When the jar cools down, the absence of air inside the jar creates the hermetic vacuum seal making proper venting doubly important.

  26. Lettie, The Jardin company that now owns Ball and Kerr labels has developed and recommends a tool for appropriately tightening the bands. It is known as The Sure Tight™ Band Tool; it secures jar bands with just the right amount of torque securing the band to the correctly. This tool is suppose to take the guesswork out of securing the band to “fingertip tight”. It fits both wide mouth and regular mouth jars and doubles as a lid and band remover.

  27. My friends from Eastern Europe add a quarter of an aspirin to garlic, green pickled tomatoes and carrots before canning. Does the salicylic acid act as a replacement for citric acid?

  28. Susan, I am sorry that your European friends are using aspirin to acidify vegetables; this is not a safe practice. Aspirin, which has salicylic acid, is not acidic enough to properly treat foods for canning. Only bottled lemon juice, vinegar, or concentrated citric acid designed for canning is recommended for adding to tomatoes by the USDA. Any other vegetable must be processed in a pressure canner as only adequate heat treatment renders a product shelf-safe. Please direct your friends to the National Center for Home Food Preservation for more information and recipes for canning safely.

  29. Hi curious as to why my canned tomatoes (with Italian spices) have two different colors in them light red to darker red. .? Top did seal after hot water bath.

  30. Rita, I think the blog explains the reason for different colors quite well. Product inside the jars is safe as long as it was processed as directed by a USDA tested and research-based recipe like those found at the National Center for Home Food Preservation. That link can also be found in the blog.

  31. Recipes call for bottled lemon juice. Why not fresh squeezed lemon juice? I freeze this juice for canning all the time.

  32. Hi Fran, Great question. First and foremost, it is a USDA recommendation. The reason for the recommendation is that bottled lemon juice has been uniformly acidified or standardized so there is a consistent and known acid (pH) level which is needed for safe canning and for making jams and jellies gel properly. When canning tomatoes, it is important to get the pH correct. And when making jams or jellies, the degree of acidity in any citrus juice added affects the natural fruit pectin’s ability to gel.The pH of fresh lemons varies a lot from variety to variety and even from lemon to lemon.

  33. I’ve been canning tomato juice for 20+ years usually about 400 quarts a year,I start off cutting tomatoes in quarters then putting them in stock pot heating and mashing about a pound+ at a time until I get my pot full and safe enough to run through juicer,then set aside until all tomatoes have been heated and run through juicer,then I put juice back in pot bring to simmer for 5+ mins. A lot of work when your doing 80 sometimes over 100 pounds at a time.my question if I juice cold tomatoes then heat the juice up will I have water separation??someone told me I’m taking to many steps just juice washed cut up cold tomatoes and then heat to a boil…sure would be nice to cut out a step…

  34. Separation is a visually disappointing issue that does not affect safety of the product. When tomatoes are cut or crushed before heating, exposure to the air activates a natural enzyme, Pectose (Pectinesterarse), found in high concentrations in tomatoes. The enzyme is activated when tomatoes are cut. This enzyme breaks down pectin which causes the liquids and solids to separate. Heating tomatoes immediately after they are cut or crushed to 180F (82C) inactivates this enzyme. This is the reason that many tested recipes direct one to cut small quantities of tomatoes and heat them in batches. Gently shaking the jars after the product has cooled for 24 hrs may bring the solids and liquid back together. Personally, I quickly skin my tomatoes and drop them into my blender jar. As soon as the blender jar is full, I puree/chop and pour them into a stock pot, heating them as quickly as possible. While they are heating, I am repeating the process until the stock pot is full. With this process, I have very little separation and I can get through quite a few pounds of tomatoes rather quickly.

  35. Thank you for explaining the separation process. I feel better about that. However, there are bubbles in the jar and worried if it is ok. After blanching and removing skin, I cut the Roma’s in half. We packed the sterilized jars and looked like we removed all the air bubbles. Our recipe book said to boil for 1 hour and 25 min, since they were raw. All jars popped.

  36. Canned whole tomatoes. All sealed. But one jar has tomato stuck to lid even after jostling. Any ideas? I figure it’s stuck in the sealed lid.

  37. Julia, if you really believe that the tomato is stuck in the seal, there is a very good chance that the seal will eventually seal. I suggest you refrigerate that jar and use as soon as possible.

  38. Hi there,
    This past year was the first year I used my mom’s tomato soup recipe. I’ve been consuming this soup for most of my life, and I decided to give my best go.
    This recipe calls for a 1/2 bushel of tomatoes, several onions, and lots of celery.
    We first dice these these tomatoes, and run the celery and onions through the food processor, which takes about 30 minutes to an hour.
    Then, we heat (electric stove) the mixture until it bubbles, and Cook until tender. This takes about 4 hours. I was told not to boil the mixture (212°f).
    Next, we run the mixture through a food strainer, and put the liquid back on the stove to heat for the thickener (cold water and flour, equal parts). Again, I was told not to boil.
    If the soup passes the taste test, we can it. Tap hot cans and tap not lids into a pressure canner on the stove for 15 minutes at 10 psi.

    The thing is, once I leave the cans to sit over night, the liquid separates. It doesn’t impact flavor of the soup, but it separates. My mom’s soup never separated, and I’m having trouble pinning down what I’m doing wrong. Any ideas?

  39. Hi Jacob, to begin, it is not usual for tomatoes to separate so the separation should not be a concern. It usually happens as a result of the tomatoes being exposed to air–the longer exposure, the greater the separation–so it is best to slip the skins as quickly as possible and get the tomatoes heating quickly as that will stop or slow down the enzyme action that causes separation. However, in reviewing your method (without the recipe), I would like to offer some suggestions to insure that your soup is both safe and tasty. To begin, you should be using a researched based recipe when it comes to canning; often old family recipes are just not safe and based upon what you write, I find procedures and ingredients that may make the recipe unsafe. The best resources for researched based home canning recipes are the National Center for Home Food Preservation website, USDA Complete Guide to Canning (online and book form), and a book which you can order, So Easy to Preserve. Now the down side of all of these excellent resources is that there is not a recipe for Tomato Soup. To remedy that, the suggestion is to make and can a Tomato and Vegetable Juice Blend (https://nchfp.uga.edu/how/can_03/tomato_veg_juice.html). Do not add flour to the canned mixture; flour is no longer recommended to be used as a thickening agent in canning. Flour tends to clump, break down when reheated, and most importantly, does not allow adequate heat penetration to the center of the jar during processing. So the method is this: use the juice blend recipe and can in pint or quart jars following exact amounts in the recipe to keep the pH correct and process according to directions taking altitude into consideration. At the time of use, make a roux of 1 tablespoon butter and 1 tablespoon flour (pints) or 2 tablespoons butter and 2 tablespoons flour (qts) then add the jar of juice and heat (it is not necessary to boil). My personal experience with this is that this makes a tasty and safe homemade tomato soup. If you like it sweeter, you can add sugar as you desire when reheating. I hope that you will give my suggestions a try and know that your soup will be safe. Thanks for contacting AnswerLine.

  40. Hi Doris, NO! NO! NO! Remove them from the pressure canner and do no disturb them for 24 hours.

  41. Hi! My question isn’t about tomato’s, but I’ve looked everywhere for some sort of answer so I’m trying here.

    I’m canning a brewed tea.
    I steep the tea leaves, lemon, oranges, spices, garlic, and a dash of ACV.

    Once steeped, I strain it and transfer the brew to jars with honey. From there, I put them in a water bath, let he temp reach 220, time it for 30 min from there, remove and let sit.
    I’ve done this countless times and never had a problem. Now all of a sudden, I’m getting what looks like liquid separation. It’s like a big clump of stuff floating in the liquid that is no longer opaque. I’ve tried changing several things and can’t seem to correct the problem! I’m no experienced canner and what I do, I’ve got from reading things and figuring it out. I desperately need help!!!

  42. Hi Brittany, thank you for reaching out to AnswerLine. I cannot specifically answer your question but can provide some insight that may help you answer your question. I feel like it has something to do with the acididity of your tea solution. When tea is overcooked (30 min of processing is a long time), tannins are released which are somewhat acidic. Honey is a combination of sugars (fructose and glucose) along with several different acids; honey is acidic by nature. You also mention the addition of apple cider vinegar, also acidic. In the presence of heat, coagulation occurs between sugars and acid. Since there are no reasearch-based recipes for cannning tea, I cannot advise you on what is a correct time and method for preparing tea so that this does not occur and that you have a safe, shelf-stable product. Lastly, perhaps there is a typo, but I want to clarify that the temperature of a water bath is that of boiling water, 212 degrees F (100 degrees C), not 220 degrees.

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