This dataset contains processed multi-omic bulk data of lung neuroendocrine tumours (lung NETs), a rare and understudied type of lung cancer. The dataset contain molecular data for 201 novel participants, comprising n=104 grade-1 and n=40 grade-2 tumours, multi-regional sequencing for 41 participants, longitudinal sampling of one participant, and reprocessed and harmonized data from previous studies of large-cell neuroendocrine tumors (LCNEC). The dataset consists of somatic variants called from whole-genome sequencing (WGS), gene expression and cell type estimates from RNA-sequencing data (RNA-seq), and M and beta values from DNA methylation arrays, along with metadata including the molecular group (Ca A1, Ca A2, Ca B, and supra-carcinoid enriched). Processed spatial transcriptomics (10X genomics VISIUM) datasets of four samples are also including, consisting of gene expression, inferred CNVs and aneuploidy status, and spatial domain and cell proportions for each spot. Note that in addition to the 201 newly sequenced samples mentioned above, the processed files also include 276 previously published lung neuroendocrine neoplasm samples that were reprocessed following the exact workflows described above in order to avoid batch effects. See Sexton-Oates et al medrxiv 2025 (https://www.medrxiv.org/content/10.1101/2025.07.18.25331556v1) for details, and the metadata.csv file, where samples sequenced for this study are denoted as “lungNENomics” in the “source” column, and reprocessed previously published samples are denoted according to the study where they were first published (first author + year of publication). Also note that corresponding raw sequencing data (fastq files for RNA-seq, cram files for WGS, and idat files for methylation arrays) is hosted on the European Genome-Phenome Archive website, study EGAS00001005979. Additionally, raw spatial data (Digital Spatial Profiling spatial proteomics and 10X Visium transcriptomics) is also hosted in the EGA study, and medical imaging data (Hematoxylin & Eosin stained whole-slide images) from the lungNENomics project is hosted in the EBI bioImage Archive (10.6019/S-BIAD3143).