There is not clear protocol. In natural products, the compound is generally only known after purification and identification. You will probably get different "protocols" from different chemists, and they work well for those people. I like to do a column screening using "wide polarity range chromatography" on my crude extract. For plants, I like to use methanol for extraction; other people like other solvents. For bacterial/fungal cultures, I like to extract with ethyl acetate, butanol, and also a column screen. This allows me to run different columns with a range of solvents so the compound has the best chance to elute, and I can see which column works well for me.

I also do a literature search to see what has been found in the organism I am extracting, and also see what sort of compounds exhibit activity in the biology I'm studying.

There is no standard protocol for natural product chemistry. It is purely dependent on your target compounds. So it differs with plant by plant. The natural product chemist has to arrive a protocol for individual type of secondary metabolites.