Two datasets are provided, the main dataset (rates of organic fertiliser added) and an ancillary spatial dataset (the regions). The main dataset gives the rates of carbon (t C ha-1 yr-1) and nitogen (t N ha-1 yr-1) addition through organic fertilisers to agricultural soils for thirteen crops and six grassland management intensities, for 24 agri-climatic regions. These agri-climatic regions represent different broad agricultural zones that correlate with elevation, as well as large biogeographical regions incorporating climatic gradients across the country. Data are provided for 35 years (1990 to 2024), for each of twelve organic fertiliser types as well as the total amounts, i.e., the sum of twelve organic fertilisers types, for carbon and for nitrogen. The data are available as two data types. Firstly, as an R data cube (OrgFert.rdata), where the dimensions are as follows: Dimension (D)1 = organic fertilisers; D2 = regions; D3 = crop / grassland type; D4 = year (1990 to 2024); D5 = carbon or nitrogen. Secondly, as 312 .csv tables (12 crop/grassland groups × [12 organic fertilisers types + ‘total’ organic fertilisers = 13] × 2 [carbon and nitrogen]); in each table are rates of carbon or nitrogen additions for each of the 24 regions, for 35 years. The file name indicates whether carbon or nitrogen inputs are given, the crop and the organic fertilisers type, e.g., the file “OrgFert_PO_DiLi_N.csv” contains data on N additions via liquid digestates to potatoes. Major crops in Switzerland that are not included are assumed to receive mineral fertilisers only, or no fertilisers. The ancillary spatial dataset is a shapefile (regions.shp) containing the 24 agri-climatic regions (attribute “code”). Descriptions of all organic fertiliser types, the regions and the crop / grassland types are given in the accompanying "Data In Brief" article.