Background: Instructor scaffolding is proved to be an effective means to improve collaborative learning quality, but empirical research indicates discrepancies about the effect of instructor scaffoldings on collaborative programming. Few studies have used multimodal learning analytics (MMLA) to comprehensively analyze the collaborative programming processes from a process-oriented perspective. This research conducts a MMLA research to examine the immediate and delayed effects of instructor scaffoldings on small groups' collaborative programming in K-12 education context with an aim to provide research, analytics, and pedagogical implications. Results: The results indicated that the instructor provided five types of scaffoldings from the social, cognitive, and metacognitive dimensions, and groups had seven types of responses (i.e., immediate uptake and delayed use) to five instructor scaffoldings, ranging from the low-to-medium and high level of cognitive engagement. After the scaffolding was faded, groups used the content from the high-control cognitive scaffolding frequently to solve problems in a delayed way, but groups did not use the instructor's scaffolding content from the social and low-control cognitive scaffoldings from the pedagogical perspective, instructors should consider scaffolding types, group states and characteristics, as well as the timing of scaffolding to better design and facilitate collaborative programming. From an analytical perspective, MMLA was proved to be conducive to understand collaborative learning from social, cognitive, behavioral, and micro-level dimensions, such that instructors can better understand and reflect on the process of collaborative learning, and use scaffoldings more skillfully to support collaborative learning. Conclusions: Collaborative programming is encouraged to be integrated in STEM education to transform education from the instructor-directed lecturing to the learner-centered learning. Using MMLA methods, this research provided a deep understanding of the immediate and delayed effects of instructor scaffoldings on small groups' collaborative programming in K-12 STEM education from a process-oriented perspective. The results showed that various instructor scaffoldings have been used to promote groups' social and cognitive engagement. Instructor scaffoldings have delayed effects on promoting collaborative programming qualities. It is highly suggested that instructors should integrate scaffoldings to facilitate computer programming education and relevant research should apply MMLA to reveal details of the process of collaboration.