Place the chicken thighs in the slow cooker crock and season with salt and pepper on both sides.
Sprinkle the garlic and onions all over the chicken thighs.
In a small bowl or glass measuring cup, combine honey, coconut aminos, sesame oil, mustard, red pepper flakes and thyme, whisking until a smooth sauce forms.
Pour the sauce over the chicken thighs and turn to coat.
Cover, then set the slow cooker to low for 4 hours or high for 2 hours.