Micronutrient content and availability in composts may be affected by the addition of wood chips or tree bark as a bulking agent in the compost feedstock. In the first part of this study, micronutrient levels were assessed in bark and wood of poplar and willow clones in a short-rotation coppice. Large differences between species were observed in bark concentrations for Cd, Zn and Mn. In the second part of the study, we aimed to determine the effect of feedstock composition and composting on Cd, Zn and Mn concentrations and availability. By means of three composting experiments we examined the effect of (a) bark of different tree species, (b) the amount of bark, and (c) the use of bark versus wood chips. In general, compost characteristics such as pH, organic matter and nutrient content varied due to differences in feedstock mixture and composting process. During the composting process, the availability of Cd, Zn and Mn decreased, although the use of willow and poplar bark or wood chips resulted in elevated total Cd, Zn or Mn concentrations in the compost. Cd concentrations in some composts even exceeded legal criteria. Cd and Zn were mainly bound in the reducible fraction extracted with 0.5M NH2OH⋅HCl. A higher acid-extractable fraction for Mn than for Cd and Zn was found. Higher Cd concentrations in the compost due to the use of bark or wood chips did not result in higher risk of Cd leaching. The results of the pH-stat experiment with gradual acidification of composts illustrated that only a strong pH decline in the compost results in higher availability of Cd, Zn and Mn.