I saw this novel at AX but all I can remember is the description.

It's about this ex mercenary or soldier who starts a bakery but no one goes to it because he looks scary. One day a young girl enters into his store.

I think it had the word automaton in the title

The novel you're looking for is "Tatakau Panya to Kikaijikake no Kanbanmusume", called "The Combat Baker and Automaton Waitress" in English.

Edit: It's got approved, so here is the MU link - Tatakau Panya to Kikaijikake no Kanbanmusume (Novel).