Since Libet's seminal observation that a brain potential related to movement preparation occurs before participants report to be aware of their movement intention, it has been debated whether consciousness has causal influence on movement decisions. Here we review recent advances that provide new insights into the dynamics of human decision-making and question the validity of different markers used for determining the onset of neural and conscious events. Motor decisions involve multiple stages of goal evaluation, intention formation, and action execution. While the validity of the Bereitschaftspotential (BP) as index of neural movement preparation is controversial, improved neural markers are able to predict decision outcome even at early stages. Participants report being conscious of their decisions only at the time of final intention formation, just before the primary motor cortex starts executing the chosen action. However, accumulating evidence suggests that this is an artifact of Libet's clock method used for assessing consciousness. More refined methods suggest that intention consciousness does not appear instantaneously but builds up progressively. In this view, early neural markers of decision outcome are not unconscious but simply reflect conscious goal evaluation stages which are not final yet and therefore not reported with the clock method. Alternatives to the Libet clock are discussed that might allow for assessment of consciousness during decision making with improved sensitivity to early decision stages and with less influence from meta-conscious and perceptual inferences.