Background: The actions of plant antimicrobial peptides (PAP) against intracellular pathogens are poorly known. It has been reported that wheat puroindolines show antibacterial activity against Staphylococcus epidermidis endocyted by macrophages. In this work, we evaluated the intracellular antimicrobial activity of PAP γ-thionin and thionin Thi2.1 produced by bovine endothelial cells against intracellular Staphylococcus aureus and Candida albicans. We used three host-pathogen models: 1) bovine mammary epithelial cells (BMEC)-S. aureus, 2) bovine endothelial cells (BEC)-S. aureus and 3) BEC-C. albicans, and evaluated the effect of conditioned media from BEC producers of PAP (γ-thionin and thionin Thi2.1). Results: In the first model, conditioned medium (CM) containing Thi2.1 completely inhibited S. aureus intracellular after 24 hrs treatment. In the second model, CM from BEC containing γ-thionin has a better effect killing intracellular S. aureus for 12-24 hrs incubations than CM from endothelial cells producers of Thi2.1; this was related with an increase of nitric oxide production (~2 times) in BEC infected and treated for 12 hrs with CM containing γ-thionin, which negatively correlates with bacterial viability. In the third model, CM containing Thi2.1 showed a more potent intracellular fungicidal activity (~85% of inhibition) at 24 hrs treatment than CM containing γ-thionin (~35% of inhibition). Conclusions: This work shows new effects of PAP to control intracellular bacterial or fungal infections.