Plants use the fertilizer to grow, and the molecules that were added in the fertilizer are certainly present in the plant and our food. In fact, the nitrogen in fertilizers is mostly made artificially through a chemical reaction known as the Haber process. The reaction takes gaseous nitrogen and hydrogen and combines them to form ammonia, a form of nitrogen that plants can use.
The fixing of atmospheric nitrogen into ammonia is a critical step in plant growth, and is done naturally by microorganisms known as diazotrophs. However, we now fix more nitrogen artificially through the Haber process than all of the diazotrophs on the planet! Like it or not, over half of the nitrogen atoms in your body were fixed through this process. Without artificial nitrogen fixation, we would not be able to feed over 1/3 of the people on the planet.
The Haber process uses 1-2% of the total world's energy. We have to get the hydrogen from natural gas, making the process highly dependent on non-renuable resources.