Bottom trawling in shelf seas can occur more than 10 times per year for a given location. This affects the benthic metabolism, through a mortality of the macrofauna, resuspension of organic matter from the sediment, and alterations of the physical sediment structure. However, the trawling impacts on organic carbon mineralization and associated processes are not well known. Using a modelling approach, the effects of increasing trawling frequencies on early diagenesis were studied in five different sedimentary environments, simulating the effects of a deeper-penetrating gear (e.g. a tickler chain beam trawl) versus a shallower, more variable penetrating gear (e.g. an electric pulse trawl). Trawling events strongly increased oxygen and nitrate concentrations in surface sediment layers and led to significantly lower amounts of ammonium (43 % 99% reduction) and organic carbon in the top 10 cm of the sediment (62 % 96% reduction). As a result, total mineralization rates in the sediment were decreased by up to 28 %. The effect on different mineralization processes differed both between sediment types and between trawling frequencies. The shallow-penetrating gear had a slightly smaller effect on benthic denitrification than the deeper-penetrating gear, but there were no statistically different results between gear types for all other parameters. Denitrification was reduced by 69% in a fine sandy sediment, whereas nitrogen removal nearly doubled in a highly eutrophic mud. This suggests that even relatively low penetration depths from bottom fishing gears generate significant biogeochemical alterations. Physical organic carbon removal through trawl-induced resuspension of sediments, exacerbated by a removal of bioturbating macrofauna, was identified as the main cause of the changes in the mineralization process.