The best way is to start with the lightest cleaning methods and work your way to the strongest if necessary. First, gently scrub the interior of the shofar with a toothbrush and water. Let dry naturally.
1. Vinegar method: Pour synthetic vinegar into the shofar and let dry naturally. Then soak the shofar in warm soapy water for twenty minutes and remove to dry. This method can be repeated once or twice.
2. Hydrogen peroxide method: Plug the shofar mouthpiece with an earplug and fill it halfway with hydrogen peroxide which will bubble as it cleans out the shofar from particles and residue. Swirl it around the horn and then pour it out. You can repeat this method once or twice, too.
3. Gravel method: Plug the ram's horn shofar or the yemenite shofar mouthpiece with an earplug and pour in some aquarium gravel, not large or sharp pieces. Plug the large end with a foam nerfball and shake it for about fifteen minutes. Remove nerfball and gravel, then replace balll, fill halfway with alcohol and shake for a minute. Remove nerfball and earplug, pour out alcohol and let dry naturally.
4. Oxi clean method: Plug mouthpiece with an earplug, fill the shofar or the yemenite shofar halfway with hot water and put a scoop of "oxi clean" inside. Plug the large end with a nerfball and let sit for an hour. Remove ball, pour out oxi clean, rinse and let dry.
5. Shofar odor neutralizer spray: non-toxic biodegradable Shofar Odor neutralizer spray will eliminate unpleasant scents from your shofar leaving it odor free. Shofar Odor Neutralizer Spray
6. Baking soda method: Dissolve a few tablespoons of baking soda in water and pour into shofar. Block mouthpiece and large end as above and shake for about a minute. Pour out liquid, rinse and allow to dry naturally.
7. GROUND Coffee: This is from one of our readers,  put 1lb of GROUND Coffee in it… Leave it in there for 3 days. It should take the smell out of it