Wash jars, lids and bands in hot, soapy water. Keep warm in the oven at a low temperature until ready to use to avoid breakage when filling with hot brine.
Divide garlic and crushed red pepper flakes evenly among jars, if using multiple. Pack vegetables and fresh thyme tightly into jars.
In a small pot, combine peppercorns, mustard seeds, salt, sugar, vinegar, and water. Bring to a boil over medium-high heat then lower to simmer for about 3 minutes to dissolve salt and sugar. Remove from heat and cool for about 15 minutes.
Pour brine into jars, making sure to submerge the vegetables. Tap the bottom of the jar on the counter to send up air bubbles. Refrigerate for at least 1 day before sampling. Pickles will intensify in flavor each day. After vegetables are finished you can use the same brine to pack the jar once more with fresh vegetables.