Limited rigorous evidence is available from sub-Saharan Africa regarding whether children who learn to read in their mother tongue will have higher learning outcomes in other subjects. A randomised controlled trial of mother-tongue literacy instruction, the Primary Math and Reading (PRIMR) Initiative, was implemented in Kenya from 2013 to 2014. We compared the impacts of the PRIMR mother-tongue treatment group in two languages with those of another group that did not use mother tongue, but utilised the same instructional components. Results showed that assignment to the mother-tongue group had no additional benefits for English or Kiswahili learning outcomes beyond the non-mother-tongue group, and that the mother-tongue group had somewhat lower mathematics outcomes. Classroom observational analysis showed that assignment to the mother-tongue group had only small impacts on the usage of mother tongue in other subjects. Advocates for mother-tongue programmes must consider such results alongside local implementation resistance in programme design.