Meta-analyses have found that working memory (WM) can be improved with cognitive training; however, some authors have suggested that these improvements are mostly driven by biases in the measurement of WM, especially the use of similar tasks for assessment and training. In the present meta-analysis, we investigated whether WM, fluid intelligence, executive functions, and short-term memory can be improved by cognitive training and evaluated the impact of possible sources of bias. We performed a risk of bias assessment of the included studies and took special care in controlling for practice effects. Data from 52 independent comparisons were analyzed, including cognitive training aimed at different cognitive functions. Our results show small improvements in WM after training (SMD = 0.18). Much larger effects were observed when the analysis was restricted to assessment tasks similar to those used for training (SMD = 1.15). Fluid intelligence was not found to improve as a result of training, and improvements in WM were not related to changes in fluid intelligence. Our analyses did however indicate that cognitive training can improve specific executive functions. Contrary to expectations, a set of meta-regressions indicated that characteristics of the training programme, such as dosage and type of training, do not have an impact on the effectiveness of training. The risk of bias assessment revealed some concerns in the randomization process and possible selective reporting among studies. Overall, our results identified various potential sources of bias, with the most significant being the choice of assessment tasks.