If using wooden skewers, soak them in water for at least 20 minutes before threading.
Whisk together the soy sauce, olive oil, brown sugar, garlic, ginger, rice vinegar, and pepper. Add the beef and toss to coat. Let sit at room temperature for at least 15 minutes.
Toss the squash cubes with olive oil and salt in a microwave-safe bowl. Cover and microwave for 3 to 4 minutes, stirring halfway, until just barely fork-tender.
Preheat a grill or broiler to high heat.
Thread the beef, squash, and onion pieces alternating onto the skewers.
Grill or broil for 8 to 10 minutes, turning occasionally, until the beef is charred and the squash is caramelized and fully tender.
Rest for 2 to 3 minutes before serving.