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• P. gigantea on Norway spruce stumps does not alter the fungal community and diversity. • Stumps treated mechanically, the effectiveness of treatment was high after 12 months. • Winter thinning does not avoid Heterobasidion infection on Norway spruce stumps. The fungus Heterobasidion annosum s.l. is one of the most destructive pathogens in coniferous forests in the Northern Hemisphere spreading during most of the year with spores and through root contact. However, especially in commercial forest land where forests are in active economic use, it is necessary to implement countermeasures against the spread of the pathogen with stump treatment. For this purpose, the effects of the biological control Rotstop and chemical control urea against Heterobasidion infection were analysed. The best practise for treatment of stumps with Rotstop is mechanical application during thinning, but stump treatment can be delayed after winter thinning due to warmer winters. We analysed the effect of Rotstop treatment on the fungal community and its diversity after mechanical and manual thinning. We found that Rotstop treatment did not significantly decrease fungal diversity at the genus level after mechanical stump treatment. The stump treatment with Rotstop was more successful in mechanically treated stumps, where the effectiveness of Rotstop treatment was 91 %. The treatment with Rotstop was more effective on the Hepatica (97 %) compared to Oxalis site type (84 %), however, the difference was not statistically significant. On the Oxalis site type, 6.0 % of all sequences per sample from Rotstop treated stumps harboured P. gigantea, while on the Hepatica site type 10 % of all sequences were identified as P. gigantea . In manually treated stumps, Heterobasidion and P. gigantea accounted for 6.4 % and 1.0 % of all sequences, respectively. Although the composition of detected taxons was different among sites treated with urea, versus sites treated with Rotstop and control areas, 60.1 % of all taxons detected in the dataset were shared among all three treatments. Fungal species richness and Shannon species diversity indexes were similar in all three manually prepared treatments (Rotstop, urea and control). Rotstop and urea manual treatments 3 months after winter thinning had no significant effect on the relative abundance of Heterobasidion . The results also indicate that only winter thinning (average daily temperature < 5℃) does not control or reduce the Heterobasidion infection from the cut side of the stump.