Soil microorganisms ensure vital ecosystem processes for agricultural production, such as maintenance and regeneration of soil fertility, regulation of pests, and resistance of plants to environmental stresses. Organic fertilization is increasingly recognized as one of the most favorable practices for soil microbial communities. However, organic waste products (OWP) might also represent a source of contaminants, including heavy metals that can accumulate in the soil. It is therefore essential to evaluate the consequences of a repeated use of these OWP on soil microbial communities. Soils were sampled from a market gardening field experiment in Dakar region (Senegal), where sewage sludge, poultry litter and cow manure digestates were applied three times a year for 7 years. These OWP presented diverse heavy metal content, sewage sludge being the highest. A dynamic sampling of 13 points was performed in 2022, to compare the short term (days), medium term (cultural season) and long term (years) effects of OWP application. We used DNA metabarcoding (16S and ITS target) and PLFA to investigate the evolution of the bacterial and fungal communities. The cumulative effect of OWP application explained the highest proportion of the total variation in soil bacterial and fungal communities (75 and 30%, respectively), followed by the time since last application (4 and 12 %) and the season (<1 and 3%). A significant increase of microbial biomass (~40 %) and richness (~75 and ~33 % for bacteria and fungi, respectively) was observed in all OWP treatments, compared to the mineral control. Changes in microbial communities were positively impacted by the increase in soil pH and organic carbon content in OWP treated soils, and negatively by the zinc content. Our study highlights that the benefits on soil microorganisms of replacing mineral fertilizers by OPW outweigh the risks due to heavy metal content after 7years of repeated inputs.