He was instrumental in the establishment of CSIRO Publishing in 1996, and in particular the journal "Invertebrate Taxonomy" (known as "Invertebrate Systematics" since the beginning of 2002). He chaired the editorial committee for the journal and was a frequent contributor. Nielsen enthusiastically advocated for a comprehensive repository of data on species and their characteristics, recognising informatics as a key to understanding and managing biodiversity. During the 1990s, he and other scientists pushed for an extensive global biodiversity resource, designed to utilise up-to-date informatics software and capable of collating data held on various separate databases. In 1999, the Organisation for Economic Co-operation and Development endorsed a proposal for the establishment of 'a global biodiversity information facility', and on 1 March 2001, the Global Biodiversity Information Facility was officially launched. As Australia's Head of Delegation for the GBIF and a founding member, Nielsen was en route to Montreal to attend the first meeting of the governing board when he died of a heart attack. The Karl Jordan Medal for lepidopterology was awarded to Nielsen by the Lepidopterist' Society in 1990, and he was later a member of the award committee. That same year he was the recipient of the David Rivett Medal from the Australian Academy of Science, and in 1992 of the Ian Mackerras Medal, awarded to him by the Australian Entomological Society. Nielsen was a member of several committees, societies, and advisory boards, was a Foreign Associate of the United States National Academy of Sciences, and a Foreign Fellow of the Royal Danish Academy of Sciences and Letters. As an author and co-author, Nielsen published eight books and monographs, and as an editor and co-editor, was involved with many more. He was also the author of over eighty other published pieces, mostly research and academic papers. The majority of his publications were on the topics of systematics, Lepidoptera, biological inventories, biodiversity, and informatics. Nielsen died in his sleep of a heart attack on 7 March 2001. He was in California for a conference, while on his way to Montreal from Australia, to attend the inaugural session of the governing board for the newly established GBIF, a project with which he'd been significantly involved. A few days after his death, and during the meeting Nielsen had been due to participate in, the GBIF Ebbe Nielsen Prize was conceived to honour his memory. The annual prize recognized a researcher who had made substantial contributions to biodiversity informatics.