Suggestions for smaller towns to stay nearby munich in september

Fussen
https://en.fuessen.de/

You'll might like Ingolstadt, 45 to 60 mins from Munich on half-hourly regional trains, on which you can use the cheap Bayern Ticket. Nicely situated on the Danube, it has some beautiful churches and well preserved defense works, and is totally untouristy. Indeed much better than Munich, which I can't find an attractive city. I used it as a base for Neuburg (15 mins on an hourly train) and Eichstätt (45 mins, also on an hourly train), both small charming towns.

I don't know if it's necessary to stay outside to Munich to escape the crowds. We stayed at a great little hotel that was just a couple blocks from the Oktoberfest grounds on a May trip. Being that there wasn't an event - like Oktoberfest - happening, the area wasn't that busy at all but we were still within quick, easy reach of the center if we'd wanted to use public transit. We're BIG walkers so chose to hoof it but you certainly wouldn't have to: there were transit stops nearby. We enjoyed the hotel, nearby restaurants and neighborhood in general very much.

Bavaria Boutique Hotel: Gollierstrasse 9, 80339 Munich, Bavaria, Germany. Clean, very comfortable rooms, helpful staff, good breakfast, balcony rooms (request), bar, enclosed outdoor terrace for al fresco drinks/breakfast. If checking TA reviews, ignore the one complaining about cramped rooms (they're not) or walk through "intimidating, difficult" area (it's not). Also take a look at booking.com reviews. We'd stay there again in a minute.

Freising is 24 minutes by regional train northeast of Munich, and 41 minutes by S-Bahn. It is in the MVV network, so a 24.30 EUR MVV group day ticket. There are also direct regional trains to Passau, Landshut, Regensburg from there. Also a local bus to Munich airport.

Freising has a red rectangle around it on my old "Strassen & Reisen" road atlas, indicating "picturesque town".

Ulm, Nuremberg, Regensburg, Augsburg, Starnburg; all are easy train rides from Munich. Where to stay is going to be much more dependent on what else you plan to do when you're not in Munich. If you're hiking the Alps stay south, if you're looking at cars go to Regensburg, if you're doing the Romantic Road then Nuremberg or Ansbach. Frankly the crowds in Munich are pretty predictable, just stay away from them.

Chiemsee is really interesting and only a short train ride from Munich. A lake with two occupied islands: Herrenchiemsee and the other is Frauenchiemsee. The last Mad King of Bavaria decided he wanted to build a replica of the Palace of Versailles on Herrenchiemsee which unfortunately he never completed. Still impressive to see, On Frauenchiemsee there is a convent and when I was there the nuns were producing a fairly palatable liqueur.
A really interesting place which can be easily tackled in a day. I highly recommend it.

BTW you could stay in Augsburg which is cheaper than Munich and is only 30 minutes away on the frequent trains.

The big question - WHEN in September ? Octoberfest will be in late September (the 21st onward, I believe)

Ooh, good catch, Laura. Oktoberfest does start on Sept. 21st.
My previous suggestion is a no go if visiting during the festival period.

I will be there during Octoberfest

Ah that kills all my suggestions - all too close.

Try Augsburg, the home of the Fuggerei.

It should meet all you requirements.

Murnau and Bad Tolz are nice little towns about an hour from Munich by train, both worth visiting on their own and on the edge of the Alps. A lot also depends on whether you intend on visiting other sites/locations from the your small town, apart from Munich itself.

Prien is an hour from Munich, Wasserburg (nice little centre), Kufstein and Salzburg, as well as being next door to Herrenchiemsee Palace. Berchtesgaden area a little further.

Garmisch-Partenkirchen, though not my particular favourite but pleasant enough and has two excellent gorges, is good as a starting block for Mittenwald, Oberammergau, Ettal Abbey, Linderhof Palace.

Check out the towns, your definition of a small town may well be different to mine.

We stayed in Dachau and took the train into Munich. We stayed at Hotel Burgmeier. It’s a short drive (about 2 miles) to each, the train station and the concentration camp.