Background: Agriculture plays a key role in Colombia’s economy. However, the sector faces persistent logistics, infrastructure, and supply chain integration challenges that hinder its development. While background studies have primarily addressed socio-economic needs and strategies to overcome these long-standing challenges, supply chain coordination remains critical for enhancing efficiency and sustainability. This study examined the impact of joint decision-making mechanisms on the logistical performance of a citrus food supply chain in Colombia. Methods: We employed agent-based modeling and simulation to evaluate three scenarios: single distribution (the current system referred to as Single-distribution), joint consolidation (Joint-consolidation), and joint consolidation–distribution (Joint-consolidation-distribution). Key performance indicators, including total logistics costs, Staytime, and load capacity utilization, were analyzed to evaluate the scenarios. Results: The joint-consolidation–distribution model emerged as the most effective, reducing logistical costs, improving load utilization, and increasing farmers’ revenues by 55.9% compared to individual sales. Consolidating harvest and distribution through a food hub improved efficiency by centralizing logistics and reducing the reliance on middlemen. Conclusions: Our findings provide actionable insights into how joint coordination enhances smallholder farmers’ economic outcomes, strengthens supply chain sustainability, and fosters community development. These results support policies promoting productive associations and local food hubs as key facilitators of market access and logistical efficiency in rural agricultural sectors.