Drosophila phagocytes participate in development and immune responses through their abilities to perform phagocytosis and/or secrete extra-cellular matrix components, antimicrobial peptides, clotting factors and signalling molecules. However, our knowledge of their functional impact on development and host resistance to infection is limited. To address this, we have used a genetic cell ablation strategy to generate Drosophila individuals lacking functional phagocytes. Our results highlight the essential contribution of phagocytes to embryonic development including central nervous system morphogenesis. Phagocytes also ensure optimal viability during post-embryonic development through immune functions. The use of phagocyte-depleted flies reveals the contribution of phagocytes in the resistance of Drosophila adults upon systemic infections with specific bacteria. Phagocytes were not involved in the expression of antimicrobial peptides by the fat body indicating a clear separation between cellular and humoral immune responses at this stage. Finally, we confirm that phagocytosis is a critical effector mechanism of the cellular arm by demonstrating that phagocytosis contributes to resistance to infection with Staphylococcus aureus in adults. Our results highlight the power of this cell ablation strategy to reveal the contribution of phagocytes to specific biological processes. We now provide a blueprint of phagocyte importance during both development and innate immune responses in Drosophila.