The development of beginning decoding and encoding skills is influenced by linguistic skills as well as executive functions (EFs). These higher-level cognitive processes include working memory, inhibition, and cognitive flexibility, and individual differences in these EFs have been shown to contribute to early academic learning. The present study extends the prior research on EFs by examining the relationship between one type of EF, cognitive flexibility, and decoding and encoding development in English-speaking kindergarteners with limited alphabet knowledge. Pooling data from two cohorts of kindergarten children who took part in a brief phonics intervention (N = 125 from 23 classrooms at one U.S. public school), we estimated the unique effect of cognitive flexibility on decoding and spelling gains, controlling for potential confounds. Results showed that initial cognitive flexibility significantly positively predicted word-level decoding and spelling gains (uniquely explaining an average of approximately 5% of the variance in gains for these measures), but the effect on decoding gains was stronger for children with lower incoming alphabet skills (5-7 letters or fewer). These findings are consistent with the earlier research on EFs and reading acquisition with older children, and also indicate that greater alphabetic skills may compensate for lower initial EF in decoding development for children learning alphabetic languages. [This paper will be published in the "Journal of Education for Students Placed at Risk (JESPAR)."]