When NeoMutt starts up it looks for two configuration files – one “ system” file and one “ user” file.

NeoMutt first reads the system configuration file, then the user configuration file. The two files are merged in the sense that "last setting wins". That is, if a setting is defined in both files, the user configuration file's value for that setting is the one that takes precedence and becomes effective.

NeoMutt searches for several different file names when looking for config. It looks for NeoMutt config files before Mutt config files and versioned config before plain config.