The potential of a new strain of Epicoccum nigrum to produce isomers of epipyrone A as pigments was investigated using solid state fermentation. A first screening of solid byproducts used as substrates revealed that exhausted sugar beet pulp maximized the production of pigments thanks to its higher pectin content. A subsequent optimization of the culture conditions using a central composite design was then carried out and allowed to determine optimal moisture content of 70% and optimal temperature of 23 °C. On the second hand, the possibility of growing the strain on a non-sterilized medium was investigated using a respirometry approach: the growth parameters of the strain of E. nigrum were compared with those of the endogenous microflora of the medium at different temperatures (23, 17.5, 12 and 7 °C). At 12 and 7 °C the fungus had shorter lag duration values than potential competitors from the substrate. Afterward, cultures were carried out in tray bioreactors (1 kg of dry medium, 30 cm bed height) at the same temperatures on previously sterilized medium and non-sterile medium. Analysis of pigments production and targeted metagenomic studies showed that, as suggested by respirometric data, at 23 and 17.5 °C, the pigments production was hindered because of the development of endogenous fungal competitors and temperature rise. On the other hand, at 12 and 7 °C, no temperature gradients and no differences could be observed in pigments production and fungal communities’ composition under both modalities of sterility. This study provides insights concerning the use of psychrotrophic microorganisms to remove the sterilization step without contamination issues, hence reducing the overall costs of a biotechnological process and improving the easiness of its implementation