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Malicious circuit modifications known as hardware Trojans represent a rising threat to the integrated circuit supply chain. As many Trojans are activated based on a specific sequence of circuit states, we have recognized the ease of utilizing an instruction sequence for Trojan activation inside a processor core as a significant security issue. To protect against this threat, we propose Control-Lock: a novel methodology for securing inter-module control signals against software-controlled hardware Trojans, even if the signals are known to the adversary during fabrication. We demonstrate the approach with a RISC-V processor infected with a denial of service Trojan. We evaluate different Control-Lock encryption schemes with regards to the security-cost trade-off. Our results show that protecting a processor against a software-controlled hardware Trojan exploiting code execution implies an area overhead of only 4.75% as well as a negligible delay and power overhead.