The cognitive learning outcomes of students on human motion system material at SMA Negeri 2 Banjar remain low, shown by an average daily test score of 67, below the Minimum Completion Criteria (70). Teachers' application of discovery learning has not been accompanied by a differentiated approach accommodating students' diverse learning styles. This study aims to describe the improvement of students' cognitive learning outcomes, determine the difference in outcomes between classes using discovery learning-based differentiated E-LKPD and those that do not, and measure the effect size of its application. A quasi-experimental method with a Nonequivalent Control Group Design was used, involving a sample of 63 eleventh-grade students out of a population of 95 students across three classes selected through intact group sampling, with class XI.A as the experimental group and class XI.C as the control group. Cognitive learning outcomes data were collected using multiple-choice tests and analyzed with ANCOVA and Cohen's effect size using SPSS 26. Results showed the experimental class obtained an average N-Gain of 0.70, compared to 0.68 in the control class, with consistent advantages in high-level cognitive dimensions (C4-C6). The ANCOVA test revealed a significant difference between groups after controlling for pretest (F = 10.054; p = 0.002), with a Partial Eta Squared of 0.144, indicating a large effect. These findings conclude that discovery learning-based differentiated E-LKPD effectively improves students' cognitive learning outcomes, particularly higher-order thinking, and can be recommended as an innovative, adaptive Biology learning medium.