Top and tail the beetroot but do not peel it. Place into a large heavy-based pan, cover with cold water and bring to the boil.
Reduce to a simmer and cook until tender, about 30 minutes. Drain and leave to cool.
Once cool enough to handle, rub off the skins, chop the beetroot into small cubes and set aside.
In another large heavy-based pan, add the lemon juice, lemon zest, chopped onion, apples, apple cider vinegar and fennel seeds.
Cook over a medium heat and simmer for about 10 minutes, until the apples have softened.
Add the cubed beetroot and return the mixture to a gentle simmer.
Add the sugar gradually, stirring well each time until fully dissolved.
Continue to cook for 25–30 minutes, stirring occasionally, until thick and jam-like.
Stir in the chopped capers towards the end of the cooking time, then season with salt and black pepper to taste.
Spoon the hot chutney into sterilised jars, tapping the jars gently on the work surface to release any air bubbles.
Place a pre-cut circle of baking paper directly on the surface of the chutney and seal with lids.