In recent years a new kind of threat, known as Hard- ware Trojan, is affecting the Integrated Circuit industry. Due to the segmentation in the production, untrusted parties involved in the supply chain may illegally inject additional hardware components, that, under specific circumstances, act for malicious purposes. While it is mostly unfeasible to identify malicious hardware tampering with in-lab testing, as a remedy, several countermeasures have been proposed, mostly based on hardware alterations of the original design, with the main drawbacks of in- creased production costs, increased area and energy consumption. In this paper, we introduce a cost effective solution, completely software-based, that minimize the chance of activation of a multi- stage trigger Hardware Trojan. The proposed approach relies on a software obfuscation mechanism, which exploits evolutionary algorithms to modify an executable program without affecting its original functionalities. Such always-changing, obfuscation routine, can be used to protect critical infrastructures and operations, at a minimum and predictable loss of performances. To show the effectiveness of the proposed technique, we developed a proof-of-concept evolutionary obfuscator and we are going to test it against a well-known real-world hardware attack scenario.