The growing availability of online multimedia instructions, such as Massive Open Online Courses (MOOCs) mark a revolutionary new phase in the use of technology for education. Considering the high student attrition in MOOCs, it is crucial to study how students engage and disengage during their learning experience in relation to the video lecture design. The present study conducted a pilot user experiment (n = 24) to evaluate in a multimodal way which video lecture design is more effective for learning. Two video lecture designs were scrutinized: voice over slides, and slides overlaid by picture-in-picture instructor video. The experimental setup included different tracking technologies and sensorial modalities to gather synchronized data from the learning experience: eye-tracker, Kinect, frontal camera, and screen recording. Among the measures, eye-gaze observational data, facial expressions, and self-reported perceptions were analyzed and compared against the learning assessment results. Based on these results, engagement is discussed regarding the different video lecture designs by connecting the observational and self-reported data to the short-term learning outcomes.