Phospholipid phosphatase 6 (PLPP6) regulates polyisoprenoid diphosphate signaling in cell activation. In response to pro-inflammatory stimuli, PLPP6 converts presqualene diphosphate (PSDP) into its monophosphate form (PSMP). Because polyisoprenoids serves fundamental roles in cell immunology, we generated mice deficient in Plpp6 (Plpp6 -/-) to investigate its role in isoprenoid remodeling and cellular responses in vivo. Naïve Plpp6-/- had lower total and cellular cholesterol levels. In house dust mite (HDM)-induced lung allergic inflammation, Plpp6-/- mice had reduced conversion of PSDP into PSMP. Plpp6-/- mice had lower numbers of lung eosinophils, neutrophils and dendritic cells (DCs) relative to WT. In addition, Plpp6-/- mice also had lower expression of type 2 cytokines and serum IgE levels. Uptake of labeled HDM by DCs in vivo was decreased in Plpp6-/- mice, and in vitro Plpp6-/- DCs uptake of labeled dextran by macropinocytosis was decreased with lower phosphoinositide 3-kinase (PI3K) expression and phosphatidylinositol (3,4,5)-trisphosphate (PIP3) formation compared to WT. Together, these results indicate that PLPP6 deficiency leads to lower cellular cholesterol levels, reduced polyisoprenoid diphosphate remodeling, decreased DC macropinocytosis and reduced allergen-driven tissue inflammation, and suggest a pivotal role for PLPP6 in mediating allergic responses to environmental stimuli.