Pierce the whole spaghetti squash 8–10 times with a sharp knife tip, place on a microwave-safe plate, and microwave on high for 12–14 minutes until tender when gently squeezed (use an oven mitt).
While the squash cooks, pat the shrimp very dry with paper towels to prevent watery containers.
Let the cooked squash cool 5 minutes, then cut in half lengthwise and scoop out the seeds.
Heat a 12-inch skillet over medium-high with half the butter (about 1.5 tablespoons).
Add shrimp in a single layer, season with salt and pepper, and sear 90 seconds per side just until pink. Remove immediately to a plate.
Add remaining butter to the same skillet with minced garlic and red pepper flakes; cook 30 seconds until fragrant.
Stir in the vegetable broth and add the spinach; cook about 2 minutes until wilted.
Use a fork to scrape the squash into strands and add to the skillet; toss with the garlic-butter mixture and season to taste.
Let the mixture cool to room temperature (about 20 minutes) before portioning to avoid condensation.
Portion the squash mixture into four meal prep containers and top each with shrimp.
Squeeze fresh lemon juice over each portion and add lemon zest if using; sprinkle with chopped parsley.
Seal once completely cooled, label with today’s date, and refrigerate.
Optional serving: add grated Parmesan after reheating.