The holistic effect of nature of science and science process skills on students’ conceptual and procedural knowledge and motivation within the context of modified guided discovery in physics laboratory

Literature emphasizes integrating nature of science (NOS), science process skills (SPS), and varied laboratory activities within guided discovery methods to enhance learning, yet empirical evidence on their synergistic effects remains scarce. This study involved a phase III tandem design with three treatment pair match groups, using a quasi-experimental approach and assessed the combined impact of <i>modified guided discovery methods</i> using implicit NOS integration, explicit approach of SPS, and diverse labs on academic achievement (conceptual/procedural knowledge) and motivation among 88 Ethiopian college students. ANCOVA and multiple regression analyses showed non-significant individual effects for NOS (*p* = 0.702 on conceptual, 0.842 on procedural, 0.986 on motivation), pedagogy (*p* = 0.830, 0.635, 0.759), and SPS (*p* = 0.568, 0.880, 0.952) on conceptual, procedural, and motivation, respectively. Interaction effects (NOS, SPS, and<i> </i>pedagogy) were also non-significant across outcomes (*p* > 0.05). However, substantial Partial eta-squared values indicated meaningful practical effects: individually, NOS (η² = 0.865 on conceptual, 0.815 on procedural, 0.658 on motivation) and SPS (η² = 0.894 on conceptual, 0.788 on procedural, 0.724 on motivation) strongly influenced outcomes; interactively, NOS*SPS had large effects on conceptual knowledge (η² = 0.711) and moderate effects on procedural knowledge (η² = 0.521) and motivation (η² = 0.524). This divergence between statistical non-significance and large effect sizes suggests the instructional model meaningfully impacts learning despite null hypothesis test results. We recommend: (1) curricular refinements to amplify effects, (2) application in diverse learning environments, and (3) supplementing traditional assessments with performance-based evaluations to better capture gains.