We evaluated the effect of cooperative learning (CL) on classroom climate during Physical Education (PE) lessons in the Elementary sublevel (2nd–4th grades; ages 6–9) in Portoviejo, Manabí (Ecuador). We conducted a cluster‑randomized controlled trial with course‑level allocation and pre–post plus follow‑up measurements. Study context and sampling frame were described using open administrative datasets from the Ecuadorian Ministry of Education (MINEDUC) and INEC, enabling stratification by school management type (public, state‑assisted, private) and location (urban/peri‑urban). The intervention delivered CL structures tailored to PE (rotating roles, team goals, promotive interaction, formative assessment) over 10–12 weeks, with implementation fidelity tracked via checklists and peer co‑observation. Primary outcomes were students’ perceptions of PE classroom climate (cohesion, teacher support, rule respect, socio‑emotional safety). Secondary outcomes included prosocial behavior, active participation/on‑task time, and fidelity. Analyses used linear mixed models with random effects at the course level, cluster‑robust standard errors, and Hedges’ g effect sizes; multilevel mediation tested the Inter vention → (prosociality/participation) → Climate pathway. Contextual characterization showed a critical mass of schools in district 13D01 (Portoviejo) and high national promotion rates (SNE 2022–2023), providing favorable conditions for implementation and interpretation. We produced descriptive figures from official data to guide planning. This study delivered a territory‑sensitive, reproducible protocol to strengthen school coexistence through PE‑based cooperative learning