Cropping practices have a great potential to improve soil quality through changes in soil biota. Yet the effects of these soil improving cropping systems on soil fungal communities are not well known. Here, we analysed soil fungal communities using standardized measurements in 12 long‐term experiments and 20 agricultural treatments across Europe. We were interested in whether the same practices (i.e. tillage, fertilization, organic amendments and cover crops) applied across different sites have predictable and repeatable effects on soil fungal communities and guilds. The fungal communities were very variable across sites located in different soil types and climatic regions. The arbuscular mycorrhizal fungi (AMF) were the fungal guild with most unique species in individual sites while plant pathogenic fungi were most shared between the sites. The fungal communities responded to the cropping practices differently in different sites and only fertilization showed a consistent effect on AMF and plant pathogenic fungi while the response to tillage, cover crops and organic amendments were site, soil and crop species specific. We further show that the crop yield is negatively affected by cropping practices aimed at improving soil health. Yet, we show that these practices have the potential to change the fungal communities and that change in plant pathogenic fungi and in AMF is linked to the yield. We further link the soil fungal community and guilds to soil abiotic characteristics and reveal that especially Mn, K, Mg and pH affect the composition of fungi across sites. In summary, we show that fungal communities vary considerably between sites and that there are no clear directional responses in fungi or fungal guilds across sites to soil improving cropping systems but that the responses vary based on soil abiotic conditions, crop type, and climatic conditions. Details on experiments related to the data is provided in supplementary materials of the related article,Fungi: DNA was extracted using the modified Power Soil protocol (Harkes et al., ), with 0.25 g soil per sample and Lysing matrix E beads tubes (MP Biomedicals). Fungal DNA was amplified using primers ITS4ngs and ITS3mix1‐5 (Tedersoo et al., , ) and purified using AMPure magnetic beads (Beckman Coulter). Polymerase chain reactions (PCRs) were performed with 12.5‐μL Hotstart ready mix (Fisher scientific) and approximately 50 ng of DNA per reaction. Dual tags were added to samples (Illumina dual indexing kits v1‐3) using seven cycles of PCR. PCR products were further purified using magnetic beads. The DNA was quantified using a Qubit fluorometer and equimolar pooled into libraries of 285 and 250 samples each. Mock community samples with eight fungal strains were sequenced along with the experimental samples. Sequencing was performed using Illumina MiSeq pair‐end 2x300bp. Here we give the OTU table and taxa files as well as report all OTUs unique to one site. Soil Chemistry: Chemical soil properties were determined by AgroCares BV (Wageningen, the Netherlands). Soils for chemical analysis were dried at 50°C using fruit dryers, crushed and sieved (2 mm sieve). One part of the soil sample was homogenized and pulverized (<0.2 mm) using a planetary micro mill with 10 clean metal balls for 3 min with speed 500 rpm. This sample was used to measure the total C and N by heating it to 900°C in the presence of O2, forming CO2 and N2, which were quantitatively measured with a thermal conductivity detector. Peak areas are correlated with validated calibration curves, to obtain element weight for C and N, which is recalculated to percentage by considering the sample mass. Total organic carbon (TOC) was measured using the Elementar Rapid CS cube (Elementar Analysensysteme, Germany) after removal and quantification of the total inorganic carbon (TIC) fraction as carbonates through acid (1 M HCl) treatment. Samples for soil texture were weighed and treated with 30% H2O2 for the removal of organic material, treated with dithionite solution (40 g/L Na2S2O4 in 0.3 M NaOAc, pH 3.8) for the removal of iron oxide, and treated with 1 M HCl for the removal of carbonates. After this sample treatment, the samples were measured with the Mastersizer 3,000 (Malvern Panalytical B.V., Almelo, the Netherlands) to determine the particle size distribution using laser diffraction. Soil pH (KCl) was determined using a pH electrode. The procedure for the extraction of soils using Mehlich‐3 solution as extractant was validated and executed according to Wolf and Beegle (), with one exception, the shaking time was increased from 5 to 10 min. The measurement of samples for the determination of bulk multi‐element concentrations in dry soil samples (RT: Real Totals) was carried out using the PANalytical Epsilon 3 ED‐XRF (Malvern Panalytical B.V., Almelo, the Netherlands). The procedure is in accordance with ISO18227:2014 and validated. The samples were prepared as pellets with a soil to wax ratio of 9:1. Lastly, cation exchange capacity (CEC) and the content of exchangeable cations (Al3+, Ca2+, Fe2+, K+, Mg2+, Mn2+, Na+, B+, Cu2+, Mo2+, Ni2+ and Zn2++) and anions (S2−, P3−) in soils were determined after extraction with hexamminecobalt trichloride solution. The procedure was validated and is in accordance with ISO 23470:2007.