Cut squash in half lengthwise, scoop out seeds and fibers.: As you cut through the tough rind you will hear a firm resistance, and the flesh inside should be pale and dense. Scoop with a spoon, removing the stringy seeds and any fibrous bits until the cavity is clean. This cleanup ensures even cooking and prevents bitter or chewy strands. A common mistake is leaving seeds behind, which can add unwanted texture and prevent the squash from shredding cleanly.
Place in a microwave safe dish and cover. Microwave 8-9 minutes.: The microwave will steam the squash quickly, yielding tender flesh. You will notice a gentle scent of cooked squash and the skin will feel softer to the touch when done. Covering traps steam so the flesh cooks through without drying. Be careful when removing the dish, it will be hot and steamy, and undercooking will leave the strands tough, while overcooking can make them mushy.
Remove from the microwave and scoop out flesh with a fork into a large bowl.: Use a fork to tease the flesh into noodle like strands, scraping along the grain until you have the desired texture. The sound is soft scraping, and the strands should separate easily, appearing glossy. Transferring to a large bowl gives space to toss the squash with pesto without crushing it. If you notice soggy clumps, the squash may have been overcooked, but gentle tossing can still salvage the texture.
Meanwhile, in a small blender combine basil, garlic, olive oil, parmesan cheese, salt and pepper and puree until smooth.: As the blender whirls, the aroma of crushed basil will rise and the mixture should emulsify into a vibrant, green sauce. The Parmigiano helps thicken and deepen the flavor while the olive oil makes the texture silky. Pulse first to chop the leaves, then stream the oil in for a creamier result. Overblending can cause the sauce to warm and lose freshness, and under seasoning will yield a flat pesto.
Combine pesto with two cups spaghetti squash (save any remaining squash for another recipe).: When you fold the pesto into the warm squash, the sauce clings to each strand and releases a fragrant herb steam. Use gentle motions to toss so the strands stay intact and the pesto coats evenly. The warmth helps the pesto open up, but avoid vigorous mixing which can mush the squash. A typical slip up is adding too much pesto at once, making the texture overly oily, so start with a modest amount and add more if needed.
Add tomatoes and season with additional salt and pepper.: Fold in the diced tomato at the end so you preserve its fresh bite and vibrant color. The contrast between warm, silky squash and cool, juicy tomato is essential for balance. Taste and adjust seasoning, noting how the tomato acidity can reduce the need for more salt. Over stirring will break down the tomato and lead to a wetter dish, so combine gently until everything is evenly distributed.