As the title suggests, I am looking for the most reliable database(s) of parent-or bedrock chemistry, e.g. the concentration of nitrogen, phosphorus and some other metals (basically plant nutrients). Since I am not a researcher in this area, it is very hard for me to determine, I would really appreciate if someone can point me to a specific source or direction.
No such thing exists.
Some of the data you're looking for may be available from government geological surveys.
For example, the Australian state of New South Wales provides this in their online map tool:
Click "Add layer", then "Geochemistry", then "All surface geochemistry". MinView from GSNSW is probably one of the better tools, anywhere in the world. Finding something like that on a global scale is impossible. You will be probably luckier with the more developed countries which invest quite a lot into this thing (like Australia and its states).