One of the ways to improve the health of your chakras is to eat for your chakras. Pay attention to which of your chakras chronically feel the most blocked or 'challenged', and consciously eat foods for those chakras.
In general, you can match the color of the chakra to the color of the food. For example, strawberries are good for the root chakra; oranges are good for the sacral chakra; yellow squash is good for the solar plexus chakra; kale is good for the heart chakra; blueberries are good for the throat chakra; and blackberries are good for the third eye chakra.
This is a good article about picking foods for chakra health: http://www.parsnipsandpastries.com/chakra-food-pairing-balancing-healing-energy-centers-food/