In order to design learning environments that foster students' research skills, one can draw on instructional design models for complex learning, such as the 4C/ID model (in: van Merriënboer and Kirschner, Ten steps to complex learning, Routledge, London, 2018). However, few attempts have been undertaken to foster students' "motivation" towards learning complex skills in environments based on the 4C/ID model. This study explores the effects of providing autonomy, competence and relatedness support (in Deci and Ryan, Psychol Inquiry 11(4): 227-268, https://doi.org/10.1207/S15327965PLI1104_01, 2000) in a 4C/ID based online learning environment on upper secondary school behavioral sciences students' cognitive and motivational outcomes. Students' cognitive outcomes are measured by means of a research skills test consisting of short multiple choice and short answer items (in order to assess research skills in a broad way), and a research skills task in which students are asked to integrate their skills in writing a research proposal (in order to assess research skills in an integrative manner). Students' motivational outcomes are measured by means of students' autonomous and controlled motivation, and students' amotivation. A pretest-intervention-posttest design was set up in order to compare 233 upper secondary school behavioral sciences students' outcomes among (1) a 4C/ID based online learning environment condition, and (2) an identical condition additively providing support for students' need satisfaction. Both learning environments proved equally effective in improving students' scores on the research skills test. Students in the need supportive condition scored higher on the research skills task compared to their peers in the baseline condition. Students' autonomous and controlled motivation were not affected by the intervention. Although, unexpectedly, students' amotivation increased in both conditions, students' amotivation was lower in the need supportive condition compared to students in the baseline condition. Theoretical relationships were established between students' need satisfaction, students' motivation (autonomous, controlled, and amotivation), and students' cognitive outcomes. These findings are discussed taking into account the COVID-19 affected setting in which the study took place.