This paper analyses the processes through which racially exclusionary policies lead to lower educational out-comes for indigenous population groups in racialised and colonial settings. Focusing on Colombia and Mozam-bique, we show that for much of the 20th century indigenous people were unable to access the same schooling as the non-indigenous population. Most indigenous children did not advance beyond very low-quality forms of education in schools run by Catholic missions. This, together with much lower public investments in the education of indigenous peoples, put indigenous children at a comparative disadvantage for the accumulation of human capital. We show this by constructing new estimates of literacy and primary education completion rates for the different ethnic groups in Colombia and Mozambique over the 20th century. In accordance with our argument, we find systematic differences in the accumulation of human capital for the indigenous and non-indigenous populations respectively