The purpose of this article is to present and test a framework for lean implementation in the agricultural sector, addressing challenges from an operational and strategical perspective. The article builds on the previous literature on the use of Lean and reports empirical data from a lean implementation project in the south-western Sweden, including interviews, observations, diaries and questionnaires. A framework is developed to examine strategic and operational perspectives on Lean Thinking. Using this framework, a number of challenges encountered in Lean implementation are presented. This article is limited to the study of Lean among a group of Swedish farms although its findings may have implications for the wider agricultural sectors. Many societal challenges are linked with agricultural sustainability, stressing the need for productive, resource-efficient, resilient and less wasteful food production. This article is the first to develop and test a Lean implementation framework in the agriculture sector. © 2018 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.