This is the second in series of studies designed to test direct and conditional effects of embedded cognitive practice in phonics instruction. Students identified in winter of kindergarten with minimal alphabet knowledge were randomly assigned to one of two conditions: explicit phonics (Plain) (n = 28) or explicit phonics with embedded cognitive flexibility practice (Flex) (n = 29). The core of both conditions was an explicit structured literacy approach: the Flex condition was differentiated by brief cognitive flexibility practice switching letter or word dimensions. Instruction was delivered individually over a six-week period. In spite of COVID-19 impacts, both treatment groups exhibited significant gains on reading outcomes. However, there were no significant differences between the conditions on growth in decoding, encoding, or cognitive flexibility. Future research should consider the timing and design of instruction to determine how cognitive abilities, as well as alphabet knowledge, contribute to acquisition of early reading skills. [This paper will be published in "Reading Psychology."]