Using your plunger, unclog the toilet completely, then flush the toilet. This will allow the toilet to refill with fresh water.
Pour 2 cups of white vinegar into the toilet bowl. The vinegar is a natural disinfecting, deodorizing and cleaning element that will remove the soil from the plunger, along with any associated odor or bacteria.
Swish the plunger in the vinegar and water mixture, agitating until all soil has been removed.
Remove the plunger from the water, and flush the toilet once more to flush away any remaining residue or particles. The vinegar will also work as a natural cleaning and deodorizing agent for the toilet bowl itself.
If necessary, rinse the plunger again in the toilet bowl water after another flush. Return the toilet plunger to its holder to dry.