This article starts by establishing a link between the nature of the threats created by jihadist terrorism and global organized crime and the investigation model used by Portuguese intelligence and police entities to detect and eliminate them. The visible manifestations of jihad terrorism and related organized crime recorded in Portugal since 2001 are also documented. The article goes on to analyze most recent theories produced on the importance of intelligence work and criminal investigation in combating these threats. On this basis, the article raises the hypothesis that Portugal’s capacity to confront these threats has been dangerously weakened by the investigation powers constraints and conflicts of jurisdiction in the national security system, the lack of effective coordination in the whole system, and delays in the necessary reforms for over a decade.