Technological advances in next-generation DNA sequencing have made using and collecting multiomics data increasingly accessible. When compared to single omics studies, multi-omics approaches offer the opportunity to achieve a deeper understanding of relevant plants hot topics, like the ones involving growth, adaptation, development, and disease progression. In this review the importance of adopting an integrated multi-omics approach is discussed and some important plant phenomena are treated. More in detail, plant stress response, diseases and senescence are described, focusing on genomics, transcriptomics proteomics, metabolomics-based research methods. Furthermore, software tools and bioinformatic resources devoted to support integrated multi-omics approaches are briefly examined and some of their limitations are highlighted. At the same time, open issues are outlined.