This study investigated the effect of explicit nature of science (NOS) instruction and explicit argumentation instruction in socioscientific and scientific contexts, on students' NOS conceptions and their argumentation skills. Undergraduate students enrolled in two sections of a science content course were assigned into two groups: Socioscientific Issues-SSI group and Scientific group. The intervention involved two stages for the explicit instruction of NOS and argumentation. In the first stage, NOS and argumentation were taught through activities and tasks for both groups. The second stage was different for the two groups, and it involved engaging participants with argumentation and NOS through SSI scenarios for the SSI group and scientific scenarios for the Scientific group. Data collection included responses to pre- and post-administration of two open-ended questionnaires as well as semi-structured interviews. Results indicated that students in SSI group mostly showed more improvement in their argumentation skills than students in Scientific group in response to SSI scenarios. As for NOS, results indicated that students in the SSI group showed more improvement in their NOS conceptions than students in the Scientific group when responding to SSI scenarios. Yet there was mostly little difference in improvement between two groups when responding to the science topics.