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Stevia is a semi-perennial crop grown to obtain the diterpene glycosides in its leaves, which are processed to manufacture non-caloric sweeteners. Anaerobic soil disinfestation (ASD) and fungicide application were evaluated for the management of stevia stem rot (SSR) and Septoria leaf spot (SLS) in lab and field experiments. In 2019 and 2021, experiments using carbon sources for ASD were carried out in microplots at NCSU (Clayton, NC, USA). In 2020/21 and 2021/22 seasons, field experiments were conducted at CSAEGRO, Mexico (MX) and CEDIT, Paraguay (PY) using a 2 × 3 factorial design with two ASD treatments and three fungicide treatments. ASD treatments included soil amended with cornmeal (MX) or wheat bran (PY) at a rate of 20.2 Mg ha−1, molasses at 10.1 Mg ha−1, and non-amended controls. Fungicide applications included chemical (azoxystrobin), organic (pyroligneous acid, PA), and a non-treated control. ASD was effective in reducing sclerotia viability of Sclerotium rolfsii in laboratory assays (p < 0.0001) and microplot trials (p < 0.0001) in NC. During field trials, the viability of sclerotia was significantly reduced (p < 0.0001) in soils amended with cornmeal + molasses or wheat bran + molasses as carbon sources for ASD. While there was no significant effectiveness of ASD in reducing SLS in 2020 and 2021 or SSR in MX 2020 field trials (p = 0.83), it did exhibit efficacy on SSR in 2021 (p < 0.001). The application of fungicides was significantly effective in reducing SSR (p = 0.01) and SLS (p = 0.001), with azoxystrobin being the most consistent and PA not being statistically different from the control or azoxystrobin. The effects of ASD on fresh yield were inconsistent, exhibiting significant effects in Mexican fields in 2020 but not in 2021. During Paraguayan field trials, ASD only significantly interacted with fungicide applications in the dry yield in 2022. In the 2020/21 MX and 2020 PY field trials, fungicides were significantly effective in enhancing dry leaf yields, with azoxystrobin showing the highest consistency among treatments and PA variable control. In conclusion, utilizing ASD alongside organic fungicides can be a valuable tool for stevia farmers when the use of chemical fungicides is limited. Further research is required to enhance consistency and reduce the costs associated with these treatments under diverse edaphoclimatic conditions. [ABSTRACT FROM AUTHOR]