Preheat oven to 375°F. Combine rinsed quinoa and 1⅓ cups broth in a medium saucepan; bring to a boil over high heat. Reduce heat to medium-low, cover and cook until the liquid is absorbed and the quinoa is tender, about 15 minutes. Remove from heat and let stand, covered, for 5 minutes. Fluff with a fork.

Meanwhile, heat 2 tablespoons oil in a large ovenproof skillet over medium heat. Add ½ cup onion; cook, stirring occasionally, until softened, about 5 minutes. Add 1 tablespoon garlic, 1 teaspoon Italian seasoning and ½ teaspoon crushed red pepper; cook, stirring constantly, until fragrant, about 30 seconds.

Sprinkle 2 tablespoons flour over the onion mixture; cook, stirring constantly, for 1 minute. Slowly stir in 2 cups milk; cook, stirring often, until slightly thickened, 2 to 3 minutes. Gradually add 12 ounces spinach; cook, stirring often, until wilted, 2 to 3 minutes. Stir in rinsed beans, 1 tablespoon lemon zest and ½ teaspoon salt. Add softened cream cheese; cook, stirring constantly, until melted and fully incorporated, 1 to 2 minutes. Remove from heat. Stir in the cooked quinoa until evenly combined. Sprinkle with 1 cup Parmesan.

Bake until the cheese is melted and the mixture is bubbling around the edges, 15 to 20 minutes. Stir in 3 tablespoons lemon juice before serving.