It may be worth trying to balance the sour flavor out using some sugar or other sweetener, it will be powerfully flavored but it's better than adding baking soda, as it has been pointed out that may change the texture and flavor in ways you do not want.
At the very least it may reduce the amount of acidity you would want to neutralize, so less baking soda would be needed.
As for what I'd do: chuck it and start over if adding sugar doesn't work.
I wouldn't make another batch and combine the two because if you combine them and it still doesn't taste good you have wasted 2 batches!
I'd start over and try to get the second batch right, then you have a better chance of getting something out of your efforts.
How much lemon juice and/or rind you need to add is dependent on personal taste, the type of apples used and their acidity (there are apples that are too sour to begin with!), and other factors like how much water is added.
A recipe in this case is a guideline, you should start with far less lemon and sugar than the recipe suggests and add more of both gradually, tasting as you go.
If you use granny smith (very, very tart) apples you'll need much less lemon and much more sugar for example.
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In theory, you could neutralize the acidity (although not the lemon flavor) by adding some sodium bicarbonate (baking soda).
The reaction products are water, carbon dioxide, and sodium citrate, which still has a sour flavor, and acts as an emulsifier.
This may change the flavor or texture of your soup in unexpected ways.
On the other hand, if you would otherwise discard the soup, this may be worth a try.
While you can try masking the flavor with other ingredients, short of something like the reaction described above, there is no way to remove the extra acidity.
Your best bet is to make another batch without the lemon juice or with reduced lemon juice, and combine them.
Of course, this will give you a very large quantity of soup.
It may not be worth trying to rescue, especially if there are no expensive ingredients in your soup.
See also: Too much sugar in soup -- how to make it less cloying?
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In general, if you want the lemon flavor, use lemon zest , but if you want the tartness, use lemon juice .
Depending on how much tartness you want in the soup, I would use a combination of zest and juice, rather than the full amount of lemon juice in the recipe.
There's really not much you can do to save your current batch, other than make a batch without the juice and combine, as another poster suggested.
cooking.stackexchange.com/users/18762/Sloan Quinn
As I noted in an answer to this question on reducing the acidity of a honey lemon drink, you really shouldn't use baking soda, as suggested elsewhere, to reduce the acidity.
This will most likely taste pretty awful.
Try adding baking soda to a lemon drink yourself and see what you think.
You have a couple more options, detailed further in this answer to a question about making a kiwi sauce less sour.
Diluting the soup with water (or something more flavourful) will reduce the acidity but may not reduce the perceived acidity .
Not your best option I say.
To reduce the perceived acidity of the soup (but not its pH), add a little sugar.
There is a possibility here that the amount of sugar needed to balance the sour combines to make a soup that is altogether too tart.
You can dampen down this sweet-sour tartness with the addition of a little salt.
Incidentally, there is no need to ruin all your soup following this (or any other) advice.
Experiment a ladle at a time and only hit the stock pot when you feel you have found an improvement.
cooking.stackexchange.com/users/1549/Chris Steinbach
If you've got too much of one of the five primary flavours (in this case sourness), you can reduce the perceived flavour by increasing one of the others:
Increase the sweetness (e.g. by adding sugar or honey)
Increase the saltiness (e.g. by adding salt or fish sauce)
Increase the bitterness (e.g. by adding greens or herbs)
Increase the umami (e.g. by adding bacon sprinkles or fish sauce)
For this kind of flavour-balancing, another option is to add some chilli - it has a similar 'distraction' effect on the taste buds.
cooking.stackexchange.com/users/14817/Vince Bowdren
I'd add calcium carbonate, not sodium bicarbonate (baking soda).
Calcium carbonate won't make the soup taste salty, and indeed if you're in the USA eating any processed or restaurant food then you most likely are eating too much sodium anyway.
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I have just made an apple soup that has lemon juice in. The problem being the lemon tartness totally overpowers the soup. How do I neutralise this???
How do I reduce the lemon acidity in apple soup?
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<soup><apples>
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cooking.stackexchange.com/users/18759/Alastair
You could add some baking soda or calcium carbonate, but this may change the texture and flavour. Another option is to mask the acidity with another primary flavour like sweetness, saltiness, spiciness, umami or bitterness. There are a number of ways to reduce acidity in apple soup. The first method is to use another primary flavour to reduce perceived acidity. The soup could also be diluted with water or a second batch of soup made without lemon juice. In general, when making apple soup, a combination of lemon juice and zest should be used to regulate acidity.
There are many ingredients you can add to the soup to reduce the acidity. Using a combination of lemon juice and lemon zest helps to balance the acidity in the soup. Make another batch of soup without lemon juice and combine with the batch containing lemon juice to reduce the acidity overall. Dilute the soup with water.