It is a good hygienic practice to keep your makeup brushes and bags clean. Bacteria may build up and cause skin irritation and infection. Many natural makeup lines use a limited amount of preservatives or antioxidants in their products and you will find that the shelf life of natural makeup is not as long as commercial brands.
Alcohol preps can be helpful and are available at most chemists. Simply wipe brushes and edges of makeup containers and lids after each use. Some chemists provide sprays as another option.
Make it a weekly habit to clean residue off brushes by washing in baby shampoo. Squeeze a few drops of shampoo onto your fingers and rub against makeup brush and rinse with water. Let the brushes dry off the edge of a table or bowl, this will help to keep the shape of the brushes and make them last longer. To disinfect dip brushes in alcohol 91% and let dry.
If your eyes become inflamed, itchy or sore after makeup application consider throwing the makeup out if it cannot be disinfected. These may include mascara and liquid eyeliner.
If you carry your makeup in a makeup bag make sure it is waterproof and can easily be cleaned with soap and water.