Nonsense-mediated mRNA decay (NMD) is important for both RNA quality control and gene regulation. NMD targets aberrant mRNA transcripts for decay and also directly influences the abundance of specific, non-aberrant transcripts in a wide range of eukaryotes. In animals, the PIK kinase, SMG1, plays an essential role in NMD, by phosphorylating the core NMD effector, UPF1. Despite being absent from the genome of the model plant, Arabidopsis thaliana, SMG1 is ubiquitous throughout the plant kingdom. Here we utilize RNA-seq to reveal the full range of processes involving SMG1 in plants. In NMD-compromised, smg1 mutant moss, 30% of multi-isoform genes produce NMD targeted transcript isoforms. Taking a machine learning approach, we show that an exon-exon junction downstream of a stop codon acts as the major feature to target transcripts to NMD and that retained intron isoforms are underrepresented among NMD targets. Furthermore, we show that SMG1 is involved in other quality control pathways, affecting DNA repair and the unfolded protein response, in addition to its role in mRNA quality control. smg1 plants have increased susceptibility to DNA damage, but increased tolerance to unfolded protein inducing agents. The involvement of SMG1 in RNA, DNA and protein quality control has major implications for the study of these processes in plants.