Research conducted on Brain-Computer Interfaces (BCIs) has grown considerably during the last decades. With the help of BCIs, users can (re)gain a wide range of functions. Our aim in this paper is to analyze the impact of BCIs on autonomy. To this end, we introduce three abilities that most accounts of autonomy take to be essential: (1) the ability to use information and knowledge to produce reasons; (2) the ability to ensure that intended actions are effectively realized (control); and (3) the ability to enact intentions within concrete relationships and contexts. We then consider the impact of BCI technology on each of these abilities. Although on first glance, BCIs solely enhance self-determination because they restore or improve abilities, we will show that there are other positive, but also negative impacts on user autonomy, which require further philosophical and ethical discussions.