For decades, universities in the Global North have been involved in so-called capacity building projects with universities in the Global South. These transnational projects, which aim to enhance teaching and research at e.g. African universities, are less studied aspects of internationalisation. This paper analyses the complex relationship between knowledge production, reproduction, and mobility in these projects. In the first part of the paper, two examples of transnational collaborative projects are analysed. The first example shows how the negotiations of scientific knowledge production and the choice of methodology situate the African partners in a dependency relation. At the same time, the very access to this methodology empowers their knowledge production. The second example shows how transnational education (through PhD-exchange programmes) can lead to a reproduction of professional academic identities and subsequently affect knowledge production. Both examples show how transnational collaboration can be both a means to independence and reinforce dependence in knowledge production in the Global South. In the second part of the paper, we ask how knowledge production varies across space and how mobility affects exchange, production and reproduction of knowledge. It ends by discussing how using geography can assist us in decolonising knowledge production and collaboration in higher education.