As students increasingly engage with digital interfaces, understanding how technology influences learning is essential. This study investigated how variations in instructional website design affect learning outcomes and identified specific design elements that enhance engagement, knowledge retention, and cognitive processing in digital environments. Two instructional websites on Python programming fundamentals incorporated distinct human-computer interaction principles to assess their impact on learning behaviors. An eye-tracking system monitored the eye gaze of participants to track user interactions. Screen recordings provided further data regarding user flows and interaction patterns. A sample of 16 students enrolled in an introductory computer science course with minimal prior experience in Python were selected to ensure a consistent baseline for learning gains and explored the websites. Participants took a 10-question quiz that reviewed material covered in the websites. They subsequently provided feedback through post-study surveys that captured their perceptions of the websites’ designs and their influence on the student learning experiences. Data analysis was conducted using ANOVA and t-tests to evaluate the influence of user interface variations on cognitive processing and retention metrics. Findings indicate that the scrollable website encouraged more review, with certain question types aligning better with specific designs. However, both websites were effective learning tools as they presented similar performance outcomes. These results emphasize the role of intentional digital design in fostering engagement, reducing visual overload, and supporting effective cognitive processing.