Collaboration among students is fundamental for knowledge building and competency development. Nonetheless, the effectiveness of student collaboration depends on the extent that these interactions take place under conditions that favor commitment, trust, and decision making among those who interact. The worldwide pandemic due to COVID-19 and the transition to emergency remote teaching have added new challenges for collaboration, mainly because now students’ interactions are wholly mediated by information and communication technologies. This study first explores the effectiveness of different collaborative relationships over performance in physics from a sample of secondary students from two schools located in rural and urban areas in southern Chile (exploratory study). We used social network analysis to map academic hierarchies as in the nominations for proficient peers in physics (i.e., physics prestige), collaboration, and friendship ties. We define a strong association if two students who collaborate shared a friendship tie. Using ordinary least squares multiple linear regression models on physics grades, we found positive effects of collaboration over grades, particularly among students working with friends (strong ties). To test whether the effects of collaboration found in the first study were stable throughout two semesters, the following year we designed a quasiexperiment in four classes from the same urban school in the exploratory study. Here, students attended hybrid school sessions where research participants were either in the classroom or participated remotely. The teacher collected the same social networks described in the first study at the end of semester 1, and two times during semester 2. In addition, we followed the same procedures to identify strong and weak collaboration from the network data on each wave of data collection. After fitting ordinary least squares multiple linear regression models, we found that collaborative variables negatively associated with grades on activity 1 (semester 1), yet at the end of the year (activity 3 in semester 2) having strong working ties became positively associated with physics grades. Interestingly, the relationship of academic hierarchies measured in physics prestige with grades transitions from positive on semester 1 to null by the end of the year. These results contribute to the literature of collaboration in physics education and its effectiveness, by taking into account social relationships and the needed time for developing beneficial collective processes among students in the classroom. We discuss these results and their implications for instructional design and guidelines for constructive group-level processes.