An increasing number of studies has investigated the latent factor structure of executive functions. Some studies found a three-factor structure of inhibition, shifting, and updating, but others could not replicate this finding. We assumed that the task choices and scoring methods might be responsible for these contradictory findings. Therefore, we selected tasks in which input modality was varied, controlled for baseline speed, and used both speed and accuracy scores, in order to investigate whether a three factor model with inhibition, shifting, and updating could still be replicated. In a group of 211 children, who were tested at the beginning of grade 1, at approximately 6 years of age, and again after 18 months, the best fitting model was not the three-factor model, but instead consisted of an updating factor and a combined inhibition and shifting factor, besides two baseline speed factors (verbal and motor). We argue that these results might indicate that the structural organization of executive functions might be different in children than in adults, but that there might also be an alternative explanation: the distinction in executive functions might not accurately represent cognitive structures but instead be a methodological artefact.