Most salsa recipes are a mixture of low-acid foods, such as onions and peppers, with acid foods, such as tomatoes. It is important when canning salsas that you are sure the acid level is high enough to prevent botulism poisoning. Many people think that tomatoes are high in acid. However, with the newer low-acid varieties it is more difficult to be sure they have enough acid to be safe to preserve using a boiling water bath canner.
Processing times are scientifically determined. It is extremely important to follow a tested recipe for tomatoes and tomato products such as salsa. Changing the amount or type of ingredients and method of preparation can influence the processing condition needed to guarantee safety. For example, adding extra vegetables to a salsa recipe can change acidity and overcooking can change the consistency. Adding drained canned crushed tomatoes that thicken the salsa or adding thickeners will not allow the heat penetration to be sufficient to process safely. Products that are not prepared according to instructions of a scientifically tested recipe should be frozen.
The type of tomato used will affect the quality of the salsas. Paste tomatoes, such as Roma, have firmer flesh and produce thicker salsas than large slicing tomatoes. Both make good salsa, but slicing tomatoes will yield a thinner salsa than a paste tomato. Salsa can be thickened by adding tomato paste.
Canning is not a good way to use overripe or tomatoes from a dead or frost-killed vine. These tomatoes will have even lower acid content. These tomatoes should be eaten fresh or used in products that will be frozen. Poor quality or overripe tomatoes will yield a very poor salsa.