Understanding the nature, density, and distribution of structural defects is crucial for tailoring the properties of atomically thin two‐dimensional (2D) materials, which is paramount for advances in nanotechnology. Ion irradiation emerges as a promising technique for defect engineering of single‐atom‐thick materials, due to its high controllability, repeatability, and accuracy. The objective is to provide a comprehensive review elucidating the impact of various irradiation parameters, such as ion mass, energy, fluence, and incident angle, on defect formation in 2D materials. However, the presence of the substrate can significantly influence defect yield and the mechanism of formation due to backscattered ions and sputtered substrate atoms. Hence, a thorough comparison of ion beam‐induced defects in both freestanding (suspended) and supported (on a substrate) 2D materials, with a focus on substrate effects is conducted. Moreover, a detailed analysis of characterization techniques suitable for each scenario will be provided. This work not only contributes to advancing the current understanding of defect formation and evolution in 2D materials during ion beam irradiation but also offers insights into selecting specific parameters for this process to create desired defects in these materials. Consequently, it has the potential to facilitate the design of nanoscale devices with tailored functionality.