This study explored how peer feedback after hands-on scientific inquiry (SI) activities affected students' SI competence over time (6 weeks) by implementing an after-school intervention program in which 188 Chinese ninth-grade students (14-16 years old) participated during their first semester. A between-subject experimental design was used for data collection, with participants randomly assigned to one treatment group (N = 120) placed in pairs or one comparison group (N = 68). Held once a week, both groups of students participated in a 40-min hands-on performance assessment developed and validated to measure SI competence. Immediately after the assessment, the treatment group undertook a 20-min paired-peer feedback session, while the comparison group received 20 min of traditional whole-class teacher feedback. The results showed that (i) hands-on SI activities accompanied by either PF or traditional collective TF improve student SI competence significantly, (ii) the effect of hands-on inquiry activities accompanied by collective TF is delayed compared to PF, and (iii) the development of inquiry abilities through the hands-on activities varied within or between the two groups. The results also showed that the development of SI abilities varied through the hands-on SI activities within or between the two groups. This study sheds light on the optimal implementation of inquiry practices, especially for cultivating student SI competence.