This study aims to investigate how working memory (WM) performances and instructional strategy choices affect learners' complex cognitive task performance in online environments. Three different e-learning environments were designed based on Merrill's (2006a) model of instructional strategies. The lack of experimental research on his framework is the main argument of this paper. The participants' WM processes with the n-back task scores were used for defining their WM performances. This study is designed as repeated measures. Thirty-five undergraduate students completed complex cognitive tasks three times. According to their WM groups, the participants were assigned to experimental conditions randomly by counterbalancing. The main results of the study indicated that although no performance differences were observed in complex cognitive tasks across instructional strategies, there was a statistically significant change observed across WM groups in favour of those who had high WM performances. The interaction effect did not have an effect on participants' overall performance. These results indicate that cognitive differences lead to different outcomes when the instructional design is set to be the same for all. Therefore, it is concluded that instructional design choices could take individual cognitive differences into account when developing adaptive e-learning environments.