Industrial inputs have replaced exact cyclic crop rotations for fertility and pest management in input-intensive agriculture, resulting in a multitude of crop sequence permutations and devastating negative externalities. Strengthening diversified and agronomically optimised crop sequences is critical to promoting sustainable practices. Comprehensive crop sequence diagnosis methods play an important role in evaluating and improving current crop sequence practices. However, recent literature on crop sequence analysis has focused on annual crops only, leading to biased results in crop sequence analysis for organic farming and livestock regions, where multi-year temporary fodder crops are a key aspect of crop sequences. In this paper, we generalise two crop sequence analysis methods —those of Leteinturier et al. (2006) and Stein & Steinmann (2018)– by including multi-year temporary fodder crops. Applying these generalised methods to a case study in the Belgian province of Luxembourg, using LPIS/IACS crop data from 2010 to 2020, we reveal significant differences in the agronomic quality of the crop sequences across the territory and between organic and non-organic plots. The inclusion of multi-year temporary fodder crops highlights the prevalence of high-diversity and high agronomic quality sequences in this livestock farming region, in contrast to the findings of Leteinturier. Maize monoculture, of low agronomic quality, and temporary grasslands, associated with high- quality crop sequences, are the main crops influencing sequence quality in the province. We observe an increase in the agronomic quality from 2010–2015 to 2015–2020, mainly due to a decrease in maize monoculture, possibly linked to the implementation of the greening of the CAP in 2015.