Slice the yellow squash into 1/2-inch rounds and thinly slice the yellow onion. Set both aside on a cutting board or in separate bowls. Having your vegetables prepped and ready before you start cooking allows you to focus on building flavor without rushing.

Melt the butter in a large skillet over medium heat. Once melted and foamy, add the sliced onions and cook for 4-5 minutes, stirring occasionally, until they begin to soften and turn translucent. This develops sweetness in the onions and creates a flavorful base for the dish.

Add the sliced squash to the softened onions from Step 2, then sprinkle with salt and black pepper. Stir everything together to combine the vegetables evenly with the butter. This initial seasoning helps draw out moisture and begin seasoning the vegetables throughout.

Sprinkle the brown sugar, crushed red pepper flakes, and fresh thyme leaves over the squash mixture from Step 3. Stir gently to distribute the sugar and spices evenly throughout. I find that adding the brown sugar at this point allows it to partially dissolve into the cooking liquid and create a subtle glaze rather than sitting on top as a garnish.

Cover the skillet and reduce heat to medium-low. Cook for 20 minutes, stirring occasionally. The cover traps steam, which gently cooks the squash through while the brown sugar creates a lightly caramelized sauce with the vegetable juices.

Remove the cover and increase heat to medium. Cook for another 8 minutes, stirring frequently, until the squash is tender and the liquid has reduced to a glossy, light glaze coating the vegetables. Taste the dish and adjust seasoning with additional salt and pepper as needed. The uncovered cooking allows any excess liquid to evaporate and concentrates the sweet and savory flavors.

Transfer the glazed squash and onions to a serving dish while still warm. Serve as a side dish alongside your favorite protein or grain.