Place chopped red onion, shallots, garlic and olive oil in a large skillet. Cook on medium heat until onions have become translucent, about 5-7 minutes.
Stir in the grated ginger and minced garlic, letting cook until fragrant, about 2-3 minutes.
Next, pour in the apple cider vinegar and honey. Stir gently to mix and coat the onions.
Stir in the granulated sugar, raisins, thyme, sea salt and pink peppercorn. Continue to cook on medium heat for about 8-10 minutes, stirring every couple of minutes. The liquid should begin to reduce and thicken.
Add the lemon juice and chopped apples. Carefully stir to distribute the apple chunks evenly. Cook an additional 5-6 minutes until the apples have slightly softened.
Remove from heat and allow to cool slightly. You can either serve your chutney warm on a prepared baguette slice or let cool completely and chill.