Remove the elderberries from the cones with a fork. Crush the pepper and mustard seeds in a mortar. Cut the chili peppers in half and remove the seeds. Peel and finely dice the onion.
Pour all ingredients into a wide saucepan and bring to a boil. Simmer the mixture for about 1 hour. Season to taste with salt, pepper, sugar or vinegar.
Fill the chutney into twist-off jars while still hot and seal tightly.