Elevated defense machinery responding to stresses often compromises plant growth. Previous studies reported that the Plant Elicitor Peptide 1 (PEP1), an endogenous danger signal triggered by biotic and abiotic stresses, affects various aspects of root development in Arabidopsis thaliana. However, a molecular mechanism underlying the action of PEP1 at the root apical meristem is yet to be elucidated. To gain an insight into this aspect, we performed a time course RNA-sequencing analysis at the root meristem following PEP1 treatment. This revealed an enrichment of a group of well-known stress-responsive transcription factors, among the PEP1-induced gene clusters. On the contrary, the PEP1-repressed gene clusters included various growth-promoting regulators. Our in-silico network analysis revealed STZ as a potential nexus between PEP1-induced stress resistance genes and PEP1-repressed growth regulators. Through various functional, phenotypic, and transcriptomic analyses, we observed that STZ and its close relatives differentially control the cell cycle, cell differentiation, and stress-responsive genes. Moreover, following the perception of stress, the transcriptional activities of STZ play a critical role in the trade-off between growth/development and defense responses. These activities depend on the dose of STZ; at the moderate dosage, STZ did not affect the root growth, though it activated various stress resistance genes, whereas at the high dosage, STZ completely exhausted the stem cell niche in the root meristem. Our findings provide valuable information about the changes in dynamic gene expression during the perception of danger signals at the root meristem and have implications regarding future engineering schemes to generate stress-resilient plants.