Precise temporal control of gene expression is critical for studying plant biology and engineering complex crop traits. Current systems enable chemically inducible regulation but rely on costly or agriculturally impractical inducers and lack the flexibility needed to regulate combinations of native loci and transgenes. In this work, we elucidate the design rules for control systems, based on Cas9 and Cre recombinase fused to the ecdysone receptor (EcR), which respond to a widely used agrochemical methoxyfenozide (MF). First, we validated the function of both circuits in transient assays and explored how transduction properties can be modulated by engineering nuclear trafficking dynamics. We next characterized both the Cas9-based and recombinase-based systems by using them to regulate fluorescent reporters in transgenic Arabidopsis thaliana plants. Here, we demonstrate systemic activation following root application of MF, validating the use of an agriculturally compatible inducer for whole-plant gene regulation. Finally, we validated the utility of the inducible Cas-based SynTF system to regulate multigene pathways and control both metabolic and developmental pathways. Together, these results elucidate design considerations for agrochemical-inducible control systems and demonstrate their utility for temporally regulating plant phenotypes. These synthetic circuits provide a versatile framework for engineering complex traits using an agriculturally compatible inducer.