Use a farm key cabinet to control access to keys for machinery and pesticide, grain, seed, and feed storage. The key cabinet can be kept in a machine shed, farm shop, or the farmhouse. The cabinet should be locked. Tag all keys indicating to what they control access. You can use a code system to tag the keys, using either numbers that match or a description. The code system would be more secure.
Keep duplicate keys in another secure location on the farm. Train all farm employees and family members to strictly follow the farm key and key storage policy. Consider changing locks on some particularly sensitive locations on the farm or ranch when employees leave the job. It is challenging to keep track of all keys and locks on the farm, but the prevention of even a single theft or malicious incident will make it well worth doing.