You can use SkeletonAnimation.CustomMaterialOverride
for this purpose, a Dictionary
mapping original materials to replacement materials:
skeletonAnimation.CustomMaterialOverride.Add(originalMaterial, newMaterial);
To clear the overrides again you can use:
skeletonAnimation.CustomMaterialOverride.Remove(originalMaterial); // clears a single material replacement
// or
skeletonAnimation.CustomMaterialOverride.Clear(); // clears all replacements.