In the current study we evaluated an afterschool nutrition education programme, called Vetri Cooking Lab (VCL), for promoting healthy and diverse eating habits among at-risk children in the Greater Philadelphia area. To understand potential programme impacts, we conducted a longitudinal analysis of survey data collected before and after participation in VCL. Main study included cooking confidence, cooking knowledge, changes in dietary consumption behaviours, and changes in vegetable preferences. Participants included students in grades 3–11 enrolled in VCL during the 2018–19 school year at VCL sites (n = 60) throughout Philadelphia, PA, and Camden, NJ. Eligible participants completed surveys both before and after participating in the programme. We found that students’ confidence and knowledge increased (P < 0.001) after the cooking intervention. Knowledge and confidence were positively associated (r = 0.55; P < 0.001). Confidence was correlated with consumption behaviour changes (r = 0.18; P = 0.022). Confidence was positively associated with consumption changes in both our adjusted (OR = 1.81; P < 0.001) and unadjusted models (aOR = 1.88; P = 0.013). Compared to Black students, White students were more likely to report consumption changes (aOR = 5.83; P = 0.013). Hispanic/Latino participants and participants who spoke Spanish had nearly three times higher odds of consumption behaviour changes (Hispanic/Latino OR = 2.55; P = 0.007; Spanish OR = 3.04; P = 0.005). Student age and gender were not associated with behaviour changes. Our research demonstrates that programmes integrating practical cooking skills education along with nutrition, food, and cooking education can improve confidence and knowledge about healthy food choices amongst children driving an overall improvement in children’s eating habits.