Two types of proton pumps in vacuolar membrane (tonoplast), the H+-pyrophosphatase (V-PPase) and the H+-ATPase (V-ATPase), establish the proton gradient that powers molecular traffic across tonoplast thereby facilitating turgor regulation and nutrient homeostasis. In this study, we discovered the function of these two proton pumps in vacuole biogenesis and auxin-regulated embryo development in Arabidopsis. While disruption of either V-PPase or V-ATPase had no obvious effect on plant embryo development and pattern formation, knocking out both resulted in defective vacuole morphology of embryo cells and abnormal embryo pattern formation. The altered initiation of cotyledon primordia indicating there would be disturbed auxin polar transportation in mutant embryo. PIN1-YFP signal in the mutant background indicated abundance and abnormal localization of PIN1 protein. Auxin accumulation marker lines DR5-GUS showed altered pattern of auxin distribution in the mutant. Pharmacological approach using BFA revealed the defects in secretory trafficking in the mutant lacking two vacuolar H-pumps, which might lead to changes in PIN1 abundance at the cell surface. Taking together, two proton pumps in tonoplast function in vacuole biogenesis/distribution and PIN1 abundance/localization thereby controlling vacuole and auxin related developmental processes in Arabidopsis embryo.