Bring 4 quarts of water to a boil in a Dutch oven. Stir in the couscous and salt, cooking until the pearls are tender, about 5 minutes. Drain well and transfer the couscous to a large bowl, covering it to keep it warm.

Wipe the pot dry, add 1.5 tablespoons of the oil, and set over medium-low heat until the oil shimmers. Add the fennel, onion, and a pinch of salt; cover and cook, stirring occasionally, until the vegetables have softened and released their liquid, about 15 minutes.

Uncover the pot and increase the heat to medium-high. Cook, stirring often, until the liquid has evaporated and the vegetables are lightly browned, 15 to 20 minutes.

Stir in the garlic and lemon zest and cook until fragrant, about 1 minute. Remove the pot from the heat, add the spinach, and cover until the leaves are wilted and bright green, about 2 minutes.

Add the warm couscous back to the pot along with the lemon juice, chives, and the remaining half-tablespoon of oil. Toss well to combine, season with salt and pepper, and serve warm or at room temperature.