Methods, apparatus, systems and articles of manufacture (e.g., physical storage media) for software defined silicon security are disclosed. Example apparatus include a trusted agent determiner to (i) determine respective reputation scores associated with a plurality of agents in a mesh network, the plurality of agents associated with a plurality of semiconductor devices, respective ones of the semiconductor devices including circuitry configurable to provide one or more features, and (ii) select, based on the respective reputation scores, a first agent from the plurality of the agents to transmit a request to activate or deactivate at least one of the one or more features. Example apparatus also include an agent interface to, in response to the request, broadcast an activation or deactivation of the least one of the one or more features to the mesh network to cause the trusted agent determiner to update the reputation score of the first agent.