Many children living in linguistically diverse low- and middle-income countries learn to read and write in multiple languages. Recent research provides implications for effective reading instruction with multilingual learners (e.g., Hall et al. in New Dir Child Adolesc Dev 166:145-189, 2019). However, there is limited empirical evidence on effective instructional practices for multilingual early grade learners who are at-risk of reading failure. The goal of our research was to examine the effect of a structured literacy intervention on literacy skills for a cohort of first grade children at-risk of reading failure as they learned to read in Kiswahili and English. Data were drawn from a larger longitudinal randomized control trial of the Primary Math and Reading Initiative in four counties in Kenya (Kiambu, Nakuru, Nairobi, and Kisumu, with 165 at-risk children identified (71 control; 94 treatment). Children in the treatment condition received daily structured instruction in letter knowledge, phonological awareness, decoding, word reading, and reading comprehension in Kiswahili and English. Children in the control condition continued with the business-as-usual approach, typically whole word instruction. Path analysis was used to examine the intervention effect of the PRIMR program through second grade. The path models further explored the within- and cross-language relationships of variables that predict oral reading fluency over time. Our analyses revealed that children in the treatment condition exhibited significantly higher growth in letter-sound knowledge for both Kiswahili and English. While growth was also observed for non-word fluency in Kiswahili and English for both treatment and control groups, there were no significant findings for this skill that can be attributed to the PRIMR intervention. Our analysis revealed that cross-linguistic elements of English reading skills contribute to oral reading fluency skills in Kiswahili. We discuss implications for aspects of structured literacy instruction essential for multilingual learners at-risk of reading failure.