Cut the yellow squash into 1/4-inch thick rounds and slice the onion into thin 1/8-inch half-moons. Set aside on a clean cutting board or in a bowl. In a small dry skillet over medium heat, toast the peppercorns, coriander seeds, and yellow mustard seeds for 1-2 minutes, stirring occasionally, until fragrant. This step blooms the spices and intensifies their flavor before pickling. Transfer the toasted spices to a small plate to cool slightly.
In a clean glass jar (about 1 quart capacity), begin layering: start with the cilantro sprigs, sliced garlic cloves, and the toasted spice mixture from Step 1. Add the red pepper flakes and fresh dill sprigs, distributing them throughout. I like to separate my spices and aromatics into layers rather than mixing them together—it creates more visual appeal and ensures better flavor distribution throughout the jar. Arrange the prepared squash rounds and onion slices from Step 1 on top of the aromatics, packing them in snugly but not crushing them.
In a medium pot, combine the cider vinegar, water, kosher salt, and honey. Bring to a boil over medium-high heat, stirring occasionally until the salt and honey are completely dissolved, about 3-4 minutes. The mixture should smell sharp and aromatic. Carefully pour the hot pickling liquid into the jar over the vegetables, making sure all the squash and aromatics are submerged. Use a wooden spoon or pickle stick to gently press the vegetables down and release any air pockets.
Allow the jar to cool to room temperature on your counter, about 1-2 hours. This cooling period lets the flavors begin to meld while the vinegar's sharp edges soften slightly. Once cooled, cover the jar and transfer it to the refrigerator. The pickles will develop better flavor after 4 hours, but I recommend waiting at least 24 hours for the best taste—the flavors really deepen after 2 days. The squash will stay crisp and delicious for up to 2 weeks when stored properly in the refrigerator.