A common way to address rural population health issues is through community stakeholders working together. Youth physical activity (PA) happens in adult-led in-school and out-of-school group opportunities that vary across communities and generally occur in isolated settings. This study explores similarities and differences in rural community system structure and collaborative process variables that help to conceptualize the collaborative impact influencing population youth PA outcomes. Stakeholders (Community 1, n = 23; Community 2, n = 26) and youth (Community 1, n = 205; Community 2, n = 213) were recruited in 2018–2019 as part of Wellscapes, a hybrid implementation-effectiveness community randomized trial. A stakeholder survey (n = 49) measured community system structures and collaboration processes. Youth completed the Youth Activity Profile to measure PA levels. More Community 1 respondents than Community 2 resided within city limits (73.9% vs. 34.6%). Collective efficacy was significantly greater in Community 1 (M = 4.0, SD = 0.5) than in 2 (M = 3.2, SD = 0.4), p