Transportation between Munich & Salzburg

Take the train. I just did the opposite direction last week, very easy. You can go to DB’s website for tickets or buy on their app.

You don't say how many are in your group, but the Bayern pass was a good option for us. It was inexpensive to begin with and even better when you add passengers. Its been about 5 years since I traveled Munich to Salzburg. I also know that Germany was doing some kind of inexpensive rail pass. In any case, rail travel between Munich and Salzburg was easy and a little over an hour.

I took the train from Munich to Salzburg and back, and it was fast and efficient both ways. The Munich Hauptbanhof (main train station) might be my favorite train station of the 40 or so I have to in Europe. I could live in the Munich train station.

Munich Hauptbanhof (main train station) might be my favorite train station

Not mine. Historically there were three separate train stations rather close together which had been combined eventually to create the main train station. But the track layout has been retained, so there is a middle section inside the big hall, and on either side there is an outer section nearly a quarter of a mile away.

If you arrive in one of the outer sections and you have to change to a train in the middle section, or worse in the other outer section, or vice versa, you need a lot of time. A short layover can be a real problem.

We took the bus which takes the same time.

We did this last summer. Took the train.

Buy a Bayern-Ticket at the S-Bahn station at the Munich airport. Take the S8 to Ostbahnhof and catch one of the regional trains from there to Salzburg.

If you take the S8 to Ostbahnhof, you don't have to go through the Hbf.

The train is your friend. While I hate Munich's current station layout, if you give yourself enough time you will be fine. The train is safe and relaxing.

Getting the train to Salzburg at the Hbf vs Ostbahnhof

The S1 S-bahn goes from the airport into town from the west. It stops first at the main station (Hbf).
From there is goes to the East Bahnhof (Ost).

The S8 S-Bahn goes from the airport into town from the east. It stops first at the east station (Ostbhf). From there it goes to the Hbf.

If you take the S1 from the airport to the Hbf, it takes about 48 minutes. The train to Salzburg starts at the Hbf, so it is waiting for a while at the platform. It is easy to board because it sits there for a while. But it takes longer to get to the Hbf than to Ost, and the train leaves from Ost after it leaves from the Hbf, so you can leave the airport on the S8, and catch a train to Salzburg, whereas you have to leave earlier from the airport on the S1 to catch the same train to Salzburg. But the train to Salzburg only stops at Ost for a minute, so you have to be ready to board.

Also, the change of platforms at Ost is relatively short, whereas, at the Hbf, you have to walk entirely across the station for your change of trains.

My vote goes as well for S8 from the airport to Ostbahnhof. Very easy to catch your train to Salzburg at Ostbahnhof.