Primary seed dormancy is a mechanism that orchestrates the timing of seed germination in order to prevent out‐of‐season germination. Secondary dormancy can be induced in imbibed seeds when they encounter prolonged unfavourable conditions. Secondary dormancy is not induced during dry storage, therefore the mechanisms underlying this process have remained largely unexplored. Here, a two‐year seed burial experiment in which dormancy cycling was studied at the physiological and transcriptional level is presented. For these analyses six different Arabidopsis thaliana genotypes were used, Landsberg erecta (Ler) and the dormancy associated DELAY OF GERMINATION (DOG) Near Isogenic Lines 1, 2, 3, 6 and 22 (NILDOG1, 2, 3, 6 and 22). The germination potential of seeds exhumed from the field showed that these seeds go through dormancy cycling and that the dynamics of this cycling is genotype‐dependent. RNA‐seq analysis revealed large transcriptional changes during dormancy cycling, especially at the time‐points preceding shifts in dormancy status. Dormancy cycling is driven by the soil temperature and the endosperm is important in perception of the environment. Genes that are upregulated in the low‐ to non‐dormant stages are enriched for genes involved in translation, indicating that the non‐dormant seeds are prepared for rapid seed germination.