This is probably going to be an unpopular opinion, but my take is: the most intuitive way to learn the notes on the fretboard is to learn to read music.

This information shortcoming of many a guitarist had confused me for years, until I realized: Intuitively knowing the notes on fretboard was a natural outcome of being taught the guitar using standard notation rather than tab. “Learning to read music” nips this common issue in the bud.

I think we, as guitarists, over complicate and mystify the fretboard, by ignoring this fundamental aspect of music education. It’s a repeating pattern of notes and they’re already in alphabetical order for us! Learning to read standard notation makes this very obvious and much easier to follow. (Not to mention it opens up the world of music for us to access and communicate clearly with other musicians etc etc.)

If I were going to add anything new to my practice routine, specifically to learn the notes on the fretboard, I’d do it by learning to read standard notation, and stop using string and fret numbers to think about what I was playing; changing my mental concept of the instrument. IME, as a teacher, this takes about a month or so to start working really well, but gains are made at each practice sessions.