We focus on the determination of point defects in semiconductor materials through constant-Fermi-level ab initio molecular dynamics and demonstrate that this technique can be used as a computer-based tool to reveal and control relevant defects in semiconductor materials. In this scheme, the Fermi level can be set at any position within the band gap during the defect generation process, in analogy to experimental growth conditions in the presence of extra electrons or holes. First, the scheme is illustrated in the case of GaAs, for which we generate melt-quenched amorphous structures through molecular dynamics at various Fermi levels. By a combined analysis that involves both the atomic structure and a Wannier-function decomposition of the electronic structure, we achieve a detailed description of the generated defects as a function of Fermi level. This leads to the identification of As–As homopolar bonds and Ga dangling bonds for Fermi levels set in the vicinity of the valence band. These defects convert into As dangling bonds and Ga–Ga homopolar bonds, as the Fermi level moves toward the conduction band. Second, we investigate defects at the InGaAs/oxide interface upon inversion. We adopt a substoichiometric amorphous model for modelling the structure at the interface and investigate the formation of defect structures upon setting the Fermi-level above the conduction band minimum. Our scheme reveals the occurrence of In and Ga lone-pair defects and As–As dimer/dangling bond defects, in agreement with previous studies based on physical intuition. In addition, the present simulation reveals hitherto unidentified defect structures consisting of metallic In–In, In–Ga, and Ga–Ga bonds. The defect charge transition levels of such metallic bonds in Al2O3 are then determined through a hybrid functional scheme and found to be consistent with the defect density measured at InGaAs/Al2O3 interfaces. Hence, we conclude that both In and Ga lone pairs and metallic In–In bonds are valid candidate defects for charge trapping at InGaAs/oxide interfaces upon charge carrier inversion. These two studies demonstrate the effectiveness of constant-Fermi-level ab initio molecular dynamics in revealing and identifying semiconductor defects in an unbiased way.