Example methods are provided for flow-based forwarding element configuration in a network environment. An example method may comprise obtaining a set of security policies associated with the group of workloads; and based on the set of security policies, identifying an allowed forwarding path between a destination and a first workload. The method may also comprise configuring a whitelist set of flow entries and sending configuration information to the flow-based forwarding element to cause the flow-based forwarding element to apply the whitelist set. The whitelist set may include a first flow entry specifying match fields and a first action to allow communication over the allowed forwarding path, but excludes a second flow entry specifying a second action to block communication over a forbidden forwarding path between the destination and the second workload. The match fields may include transport layer information and network layer information.