Microwave 2 cups water in a microwave-safe 1-quart measuring cup on high 3 minutes. Submerge chile in hot water. Let stand until soft and pliable, about 10 minutes. Drain; stem and seed chile.
Combine chile, onion, 2 tablespoons oil, harissa, lemon juice, and salt in a blender. Process until smooth and creamy, about 20 seconds. If needed, add 1 tablespoon water to thin.
Using a silicone spatula, scrape marinade into a gallon-size ziplock plastic bag. Add chicken, and stir to coat well. Seal and chill 4 hours or up to 18 hours.
Thread chicken onto 4 (8- to 12-inch) skewers (keep chunks close to one another, forming a column of meat, to ensure juicy results); bring to room temperature, about 1 hour.
Prepare a hot fire in a charcoal grill or preheat a gas grill to high (450°F to 500°F). Alternatively, heat a lightly oiled grill pan over high. Gently blot excess marinade from chicken to ensure a nice sear. Brush chicken with remaining 1 tablespoon oil.
Grill skewers, turning every 2 minutes, until chicken is lightly charred and cooked through, about 14 minutes. Let rest 5 to 10 minutes. Garnish with chives, if desired.
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