It is an undeniable fact that biometric recognition systems are susceptible to different software-related or template attacks at different vulnerable points in the biometric authentication system. However, these attacks are frequently overlooked, implying one of two possibilities: either researchers and biometric stakeholders have forgotten or simply ignored the consequences of these attacks, or they are unaware of some of these threats. Meanwhile, if biometric systems do not have the required protection, these attacks can lead to biometric system compromise and consequently the loss of sensitive personal data, which is irreplaceable and irrevocable. Therefore, considering the significance of the implications posed by these threats, researchers and biometric stakeholders have, over the last two decades, proposed different methods to mitigate some of the attacks, while a large number of the existing attacks are left unattended to. Hence, we deemed it paramount to bring this to the attention of the research community. This article is an effort to emphasize the implications of these attacks, exploit the threat approach based on attackers’ knowledge, and consolidate them into a single, thorough, and comprehensive review together with recent state-of-the-art protection mechanisms that are put forward to mitigate these threats. Moreover, a comparative performance analysis of these protection mechanisms and other possible countermeasures to the attacks is given. It is expected that this survey will, on the one hand, be a wakeup call to the biometric template protection research community, thus drawing their attention to the task at hand. On the other hand, an awareness to the ordinary users and biometric stakeholders on the risks posed by these threats.