The energy for fertilizer is mostly in the nitrogen fertilizer. The energy input here is to make hydrogen for the Haber-Bosch process. This hydrogen can come from renewable sources ("green hydrogen"), and this would be an excellent way to counter long term variability in renewable output.

That the hydrogen currently comes from natural gas is no argument it must come from natural gas, any more than cars currently using petroleum derived fuels would imply they must use petroleum derived fuels.