Assemble your ingredients and prepare your water bath canner and jars.
In a large Dutch oven, combine tomatillos, onion, peppers, vinegar, lime juice, garlic, optional cilantro, salt, and red pepper flakes. Bring to a boil over high heat, stirring constantly to prevent scorching. Reduce heat and simmer, stirring frequently for about 15 minutes. Tomatillos, onions, and peppers should be softened and ready for the next steps.
Note: If you desire a smoother salsa, use an immersion blender to blend before proceeding.
Ladle hot mixture immediately into prepared jars, leaving ½ ” headspace. Use a wooden skewer to remove any air pockets and readjust headspace if needed. Wipe jar rims and threads with a moistened towel. Cover with two-piece lids. Screw bands to finger-tip tight.
Place jars onto a rack in the canner. Water must cover jars by 1 to 2 inches. Cover canner, and bring water to a boil. Once boiling, process jars for 15 minutes (adjusting for altitude, see notes). Turn off the heat and let jars sit in the canner for 5 minutes. Remove jars and place them upright on a towel to cool completely. After the jars cool, check seals by pressing the centers of lids with your finger. If the lid springs back, the lid is not sealed and refrigeration is necessary.
Let prepared jars stand at room temperature for 24 hours. Salsa flavors will mellow over time. Store unopened salsa in a cool, dry place for up to 1 year.