Child undernutrition remains a critical public health challenge in fragile and conflict-affected settings, where community-based delivery systems play a central role. This study assessed the effectiveness of the functional capacities of Community Animation Cells (CAC) in improving the nutritional status of children under five in South Kivu. Methodology: A quasi-experimental study with a non-randomized control group was conducted in the Bunyakiri Health Zone, comparing intervention and control areas. A total of 280 households with children aged 0–59 months were surveyed at baseline and endline. Quantitative data were analyzed using Difference-in-Differences models with Poisson regression and generalized estimating equations to account for clustering, complemented by qualitative thematic analysis. Results: Households exposed to strengthened CACs showed significantly higher odds of optimal infant and young child feeding practices, including continued breastfeeding up to 24 months (aOR = 1.044; p = 0.032) and adequate meal frequency (aOR = 0.689; p = 0.045). Hygiene practices such as handwashing at critical times were strongly associated with CAC activities (aOR = 1.193; p = 0.002). By April 2024, exclusive breastfeeding in the intervention zone reached 93.6% compared with 58.2% in the control zone, while children with MUAC > 125 mm increased to 95.5% versus 58.0%. Difference-in-Differences analyses confirmed a statistically significant net intervention effect on key nutrition indicators. Conclusion: Strengthening CAC functional capacities significantly improved nutrition-related practices and nutritional outcomes among children under five. Scaling up CAC-based interventions with sustained supervision and reliable nutrition supply systems is recommended to enhance community-level nutrition impact.