Cognitive control dysfunctions are thought to contribute to the onset and maintenance of depression. However, the causes and nature of these dysfunctions remain unknown. Here, we critically review contemporary research on cognitive control in depression. We identify three main conceptual issues in this field: (a) uncritical use of the tripartite model, (b) reliance on descriptive explanations, and (c) lack of integration with emotional and motivational impairments. Recent advances in cognitive neuroscience offer possibilities to resolve these issues. We review this progress focusing on the ability to detect the need for control, the role of motivation, and the flexibility-stability balance. We propose that depression-related dysfunctions arise from issues in detecting when, how, and for how long to engage in goal-oriented processing. In conclusion, we argue that integrating advances in cognitive neuroscience into clinical research can help to move from a descriptive toward a more mechanistic understanding of cognitive dysfunctions in depression.