This article looks at how the Best Available Technology Not Entailing Excessive Costs (BATNEEC) can be implemented in practice using the ammonia regulation in Denmark as an example. The reductions of ammonia emissions in Denmark have been achieved mainly through command and control measures. The analysis in this paper shows how cost-effectiveness analyses (CEA) and analysis of the cost for the farmers (affordability) can be used to point out relevant BAT (Best Available Technology) technologies. The article discusses how the cut-off values are to some extent political as it can be difficult to set objective cut-off levels for the sector costs. The article describes different approaches on how to calculate affordability and finishes with a description of the final regulation as it has been implemented in Denmark. It shows that a stricter emission target on larger farms has counteracted the economics of size. The implication is that the abatement costs are similar on all farms. The wider implication of the findings suggests that the actual implementation of the BATNEEC at a national level can be counteracted if the local regulator has to perform case-by-case analysis. The case-by-case analysis might give more cost effective solutions, but it increases the administrative costs and delays the acceptance procedure. The article shows that the BATNEEC implementation approach is successful, although it requires some political and administrative choices to be able to push new technology in a cost efficient manner.