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In the present study, we isolated and identified a new fungus, Aspergillus sp VM-1 from banana pseudostem waste. The fungal strain, Aspergillus sp. VM-1 was grown on a substrate (banana pseudostem, cottonseed hulls and cottonseed meal in the ratio of 60:30:10, respectively) for 7 days and the crude enzyme was extracted from the fermented substrate. The pectinase activity in crude enzyme extract was 551 (U/ml). The crude enzyme extracted from Aspergillus sp. VM-1 was evaluated for bio-scouring of non-spinnable cotton. The non-spinnable cotton taken in the study was short staple cotton (SSC), cotton linters (CL) and non-woven cotton fabric (NWCF). The maximum absorbency (2 s) in non-spinnable cotton was achieved under optimized process conditions: enzyme extract level (40%), temperature (40 ± 2 °C) and time (40 min). The quality parameters of bio-scoured cotton meet the Indian Pharmacopoeia (IP) standards. A solid state fermenter was designed to scale-up the crude enzyme production up to 30 l. This is the first report on bio-scouring of under-utilized short cotton fibres at lower temperature (40 ± 2 °C). The present study offers a simple and eco-friendly bio-scouring process as an alternative to toxic chemical scouring of under-utilized short staple cotton fibres., Supplementary Information: The online version contains supplementary material available at 10.1007/s12649-021-01621-9., Competing Interests: Conflict of interestThe authors declare no conflicts of interest, or competing financial or scientific interest., (© The Author(s), under exclusive licence to Springer Nature B.V. 2021.)