The RNA degradome is composed of assorted RNA degradation intermediates derived from diverse RNA degradation pathway. In 2016, we reported that the plant RNA degradome contains in vivo ribosome footprints. In this study, we further demonstrate that exon junction complexes (EJCs) are able to protect mRNAs against 5'-3' degradation resulting in marked footprints in the RNA degradome. In addition to Arabidopsis, in vivo EJC footprints were also observed in the degradome datasets of rice, worm and human cells, indicating that this phenomenon is conserved across species. Because EJCs are deposited on mRNAs during splicing and displaced by ribosomes in the pioneer round of translation, EJC footprints can serve as markers for the mRNA degradation before steady-state translation. Predominant EJC footprints were observed in hundreds of Arabidopsis nonsense-mediated mRNA decay (NMD) targets which are presumed to be destroyed during the pioneer round of translation, validating this possibility. NMD is important in plant immune response and pathogen defense, but NMD targets were poorly defined due to the lack of suitable methodology. Here, we show that EJC footprints can be used to validate potential NMD substrates and inference of NMD activity. We also demonstrate that cleavage guided by some microRNAs (miRNAs) can result in EJC footprint accumulation on mRNAs, indicating that plant miRNAs can destabilize EJC-bound mRNAs prior to translation. Together, this is the first work reporting the presence of EJC footprints in the RNA degradome, and the analysis of EJC footprints in the RNA degradome revealed new insights into NMD and miRNA regulation in plants, demonstrating new applications of RNA degradome data.