Targeted gene silencing is an essential component of plant biotechnology. RNA interference is often employed for targeted gene silencing in plants. However, it suffers from off-target effects and unstable gene suppression in many cases. In recent years, engineered nuclease-based tools, such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), have been developed to induce site-specific genome modifications. However, these approaches require much time and labor for extensive screening of mutants. We have recently reported that the activities of dimeric transcription factors are competently suppressed by genome-encoded small interfering peptides (siPEPs) that competitively form nonfunctional heterodimers in plants. In addition, some splice variants of transcription factors also act in a similar manner to negatively regulate the activities of specific transcription factors. We designated the siPEP-mediated suppression of transcription factors peptide interference (PEPi). Based on our previous observations, we also developed an artificial siPEP (a-siPEP) approach and evaluated its application for the targeted inactivation of transcription factors in the dicot model, Arabidopsis, and monocot model, Brachypodium. We designed a series of potential a-siPEPs of two representative transcription factors SUPPRESSOR OF OVEREXPRESSOR OF CONSTANS 1 (SOC1) and AGAMOUS (AG) that function in flowering induction and floral organogenesis, respectively. Transgenic plants overproducing a-siPEPs displayed phenotypes comparable to those of gene-deficient mutants. Collectively, our data demonstrate that the siPEP tool is an efficient protein knockout system for inactivating specific transcription factors, and other multimeric enzymes and membrane transporters as well, in plants. We will discuss about the global application of the siPEP toll to other plant species and potential advantages over other gene manipulation tools.