Will my armpits need to detox when I change to a natural deodorant

In short, probably yes.  Here is a brief rundown of what to expect if you have just given up your commercial antiperspirant.

Using a natural deodorant can take up to 4 weeks to be effective, especially if you have been using a commercial antiperspirant. This is how the transition phase usually works:

Week 1 - At first all goes well.

Week 2 - Armpit bacteria begins to change, you may notice armpit odour. Most people give up at this stage thinking it isn't working.  But be patient.

Week 3 - Armpit bacteria begins to re-balance.

Week 4 - You should be fully adjusted now.

Each stage of the detox may vary depending on your body's chemistry and the different stages you are going through in your life.  ie: adolescence, pregnancy, diet etc.