One of the key issues discussed within the fields of public administration and food governance, is how to achieve coordinated implementation of cross-sectoral and crosscutting policies. The article addresses this issue by systematically comparing the public management of animal welfare in Norway and Sweden. Animal welfare has become an increasingly important issue in food governance, attracting much attention from academics, political decision-makers, as well as from NGOs, consumers, and the public. Animal welfare is a cross-cutting topic, involving different parts of the agri-food governance system (government agencies, levels of government, farms, slaughterhouses, transport-systems, marketing and advertisement etc.), as well as raising a number of important cross-cutting questions such as ethical aspects, the choice of legal tools, compliance mechanisms, and the challenge of achieving uniform inspection and control. Thus, a study of the management of animal welfare is well apt, to address the basic and underlying research questions in this article: How to deal with the challenge of coordination? What are the relevant preconditions for achieving uniform management and compliance with public set goals in the agri-food governance system? The first part of the paper describes the Norwegian and Swedish management models for animal welfare thus identifying the organizational structures of the systems. The second part describes the use of different techniques, such as information, dialogue and sanctions, in order to ensure compliance with animal welfare legislation thus identifying the regulatory tools of the systems. The third part focuses on one particular case of animal welfare management, namely the interpretation, application and enforcement of EU legislation concerning the transport of animals to slaughter. By comparing how Norway and Sweden have implemented and managed the same EU rules, we intend to identify factors, which may explain differences and similarities between the two countries. The framework used for the comparison is inspired by literature on new public management and vertical and horizontal coordination (Metcalfe 1994; Scharpf 1994; Christensen and Lægreid 2008; Peters 2015). Consequently, the article highlights two dimensions in the categorization and analysis of the Norwegian and Swedish management system: First, the fragmented-coordinated dimension (to what extent authority and responsibilities are dispersed across different sectors and public agencies), and second, the centralized-decentralized dimension (to what extent authority and responsibilities are delegated to lower level of governance). Thus, managements systems may be more or less coordinated horizontally (more or less fragmented) and more or less coordinated vertically (more or less decentralized). One core assumption is that well- coordinated and integrated systems are more likely to enhance uniform enforcement of and compliance with public policies than fragmented and decentralized systems. The data used for the article includes public documents, reports, guidelines, legislation and available literature, supplemented by interviews and Norwegian surveys of food safety/animal welfare authorities.