Combining scientific and traditional knowledge is crucial to understand environmental systems across circum-Arctic regions, where climate change is most striking. However, building collaborative partnerships between visiting scientists and local, indigenous traditional knowledge holders in Northern communities presents challenges. The workshop “Community-based Research: Do`s and Don`ts of Arctic Research” was organized as an IASC cross-cutting initiative at ICOP2016 in Potsdam, Germany, to facilitate dialogue between Early Career Researchers (ECRs) and Northern residents. This workshop resulted in a diverse list of considerations and sustainable practices to improve traditional and scientific knowledge exchange, and collaborative Northern research. An extensive list of positive (Do`s) and few negative recommendations (Don`ts) was generated together with ECRs and Arctic representatives. Many good ideas on research design, active communication and community involvement developed from fruitful discussions. This study provides an example of bottom-up strategy development in order to enhance knowledge transfer between scientists and northern indigenous communities.