Brain-computer interfaces (BCIs) allow direct communication between one’s central nervous system and a computer without any muscle movement hence by-passing the peripheral nervous system. They can restore disabled people’s ability to interact with their environment, e.g. communication and wheelchair control. However, to this day their performance is still hindered by the non-stationarity of electroencephalography (EEG) signals, as well as their susceptibility to noise from the users’ environment and from their own physiological activity. Moreover, a non-negligible amount of users struggle to use BCI systems based on motor imagery. In this paper, a new method based on the path signature is introduced to tackle this problem by using features which are different from the usual power-based ones. The path signature is a series of iterated integrals computed from a multidimensional path. It is invariant under translation and time reparametrization, which makes it a robust feature for multichannel EEG time series. The performance can be further boosted by combining the path signature with the gold standard Riemannian classifier in the BCI field exploiting the geometric structure of symmetric positive definite (SPD) matrices. The results obtained on publicly available datasets show that the signature method is more robust to inter-user variability than classical ones, especially on noisy and low-quality data. Hence, this study paves the way towards the use of mathematical tools that until now have been neglected, in order to tackle the EEG-based BCI variability issue. It also sheds light on the lead-lag relationship captured by path signature which seems relevant to assess the underlying neural mechanisms.