Putting down Lime in horse stalls is one way to control the ammonia smell in stalls used frequently. Crushed limestone helps inhibit bacteria growth, and helps relieve the ammonia smell in a closed horse stable. Lime should be applied to horse stalls approximately every six months, but the frequency of use should be relative to how frequently the stall is use. For example, stalls with horses in them all the time should be limed the more frequently than stalls that are only use occasionally.