Potato production in low-income countries is threatened by seed degeneration, i.e., the accumulation of seed-borne diseases and pests in potato seed tubers when these are vegetatively propagated over consecutive cycles, leading to a reduction in seed quality and yielding ability. Agroecological settings and seed recycling (on-farm propagation over consecutive cycles) determine the process of seed degeneration. However, it is poorly understood how these factors affect this process. Therefore, to reduce this knowledge gap, we analysed two datasets collected in Ecuador, one from a multi-annual field experiment and one from a farmers’ seed study. The experiment, carried out from 2013 to 2016, aimed to assess seed degeneration at agroecological settings present in three different altitudes. The farmers’ seed study, in which 260 farmers were surveyed in 2018, aimed to understand potato seed degeneration in farmers’ fields under diverse agroecological settings. Our results of the multi-annual field experiment showed that agroecological settings have a heterogeneous influence on the presence of seed-borne diseases and pests. We also found that both the agroecological settings at the three altitudes and the number of on-farm propagation cycles affected the rates at which seed-borne diseases and pests on the seeds increased and yield decreased. However, the farmers’ seed study challenged these results by indicating that this was not clear on farms. Combining these results, this article shows that agroecological settings and seed recycling only partially explain the process of seed degeneration. This suggests that more research about seed degeneration needs to also take place under farmers’ conditions to fully understand the complex of potato performance factors. We expect that such research will support the design of improved seed interventions, while simultaneously it may generate discussion about when potato seed degeneration plays an important role in productivity.