The particulate nature of matter is identified in science education standards as one of the fundamental concepts that students should understand at the middle school level. However, science education research in indicates that secondary school students have difficulties understanding the structure of matter. The purpose of the study is to describe how engaging in an extended project-based unit developed urban middle school students' understanding of the particulate nature of matter. Multiple sources of data were collected, including pre- and posttests, interviews, students' drawings, and video recordings of classroom activities. One teacher and her five classes were chosen for an in-depth study. Analyses of data show that after experiencing a series of learning activities the majority of students acquired substantial content knowledge. Additionally, the finding indicates that students' understanding of the particulate nature of matter improved over time and that they retained and even reinforced their understanding after applying the concept. Discussions of the design features of curriculum and the teacher's use of multiple representations might provide insights into the effectiveness of learning activities in the unit.