<div><p>Applying by-products as soil amendments to agricultural systems is growing in popularity. We aimed to assess the efficacy of some contemporary by-products to provide nutrients to crops as well as the potential harm of adding toxic elements to the environment. Four different by-products widely available in Northern Europe were tested for their effects on two nutrient-poor agricultural soils in terms of increasing available macro- and micro-nutrients as well as toxic elements. Assessing soil microbial community as a sensitive tool for evaluating soil quality was conducted with the focus on microbial activity, carbon metabolism and on <i>Rhizobium/Agrobacterium</i>. Wood ash increased pH and Ca<sub>EDTA</sub>, K<sub>EDTA</sub> and Mg<sub>EDTA</sub> in the soils. The only increase in EDTA-extractable micronutrients in the soils was observed by applying pot ale, increasing Cu. None of the amendments increased the availability of Pb and Cd in the soils. Soils amended with the by-products thus remained similar to the unamended control but were quite different from fully mineral fertilised soils. There were no detectable adverse effects on the physiological and genetic profiles of microbial communities. The by-products were moderately beneficial and did not change the soil microbial community as much as the fully fertilised treatment with mineral fertilisers. Changes in the microbial community profiles were probably due to direct effects on microbes limited by K, Ca and N as opposed to indirect effects on plant growth. This is potentially significant in understanding how to improve impoverished and marginal soils as microbial activity affects many other ecosystem functions.</p></div