Background: Organic amendment improves soil fertility affecting microbial diversity as well as the relative abundances of bacteria and fungi and as a consequence the agricultural production. Although fungal and bacterial taxa are often grouped together, they may respond differently to fertilization. Studies are needed, as a single time-point sampling cannot give details on the magnitude, stability and dynamics driving the taxonomic and potential functional of the fungal community after nutrient-induced disturbances. Here, we aim to assess how nutrient enrichments with addition of vinasse shift environmental conditions to drive fungal community assembly during soil establishment and further influence the temporal dynamics of these communities by examining one-year sugarcane field experiment with multiple pulse disturbances (application of vinasse 30 days before and together with N application). Results: Organic residue vinasse applied alone or 30 days prior to mineral N resulted in similar changes in the fungal community. We also found a stronger impact on fungal community when vinasse and mineral N were applied as a single pulse disturbance. From the trophic guilds aspect, organic amendment with vinasse was found to increase the abundance of the saprotrophs, species capable of fungal denitrification, and both fungal with copiotrophic and oligotrophic lifestyle. Furthermore, the changes in fungal community were not correlated to bacterial community. Conclusion: The fungal community was neither resistant nor resilient to organic and inorganic amendments over one-year sampling and more time is needed to check for their composition recovery. Our findings provided the first insights into the immediate and delayed response through a year of field experiment disturbed with organic enrichment.