Chamonix &Annecy on September

Getting between Geneva, Annecy, and Chamonix is fairly straightforward using
either bus or train. There are some different opinions on the efficiency, cost,
and scenic options for each, but in general either one works.

All the villages in the Chamonix area you mention are all part of the Chamonix
Valley. If you buy a Mont Blanc pass, train and bus travel along the valley is
included. I would definitely consider purchasing a pass, as it gives you
access to all gondolas and lifts, and allows you multiple chances to go up
the Aiguille du Midi gondola, which can often be affected by weather. There
is no need to consider staying in multiple villages in Cham since the train
can get you to any of them should you want to visit. But I think Chamonix
town is probably the best choice.

If you just want to wander around, Annecy is perhaps good for 3 days and
Chamonix 2. But if you are into hiking and mountain scenery, I might reverse
it.

Note that Chamonix has perhaps the most mountain hiking options anywhere
in the world. This includes nice easy trails, and some pretty technical ones.
Don't just wander out without checking a map or doing your research, lest you
end up on a trail much more difficult than you had expected.

I can offer my opinion, having traveled solo (although early June, 2 years ago) to both for 4 days.
The weather can be very changeable so I would suggest longer in Chamonix for your outdoors time. One day began with chilly temps and some rain (and a blizzard up above!) but I borrowed an umbrella from the hotel and just walked along the pretty river- you can go as far as a nearby little town for coffee. But that afternoon was just beautiful weather. It's one long street to the co-located bus and train stations. You could use day tours for the surrounding area.
I can't remember which of the two bus companies I used but reserved online and it was comfortable and about two hours and fifteen minutes to Annecy. It was about 3/4 of a mile walk through the modern town to the historic area from the station.
https://fr-alpes.fr/hotel/dupalais
This hotel was the highlight! You are literally in the middle of the pedestrianized old town with the Instagram/postcard view (ask for a room with a view).
I think one full day (stay two nights) is ample. There really is just the experience of strolling the narrow streets. When I was there it was very, very crowded, especially on the weekend. Crowded as in not being able to easily walk!
I rented a bike for an afternoon and rode to a cafe almost at the end of the lake, which was wonderful (and not crowded).
These are only my impressions! You could also take your day trips from Annecy and use it as your base.
For the beauty and hiking, though, I suggest Chamonix. And that hotel in Annecy!

I did GVA-CMX-Annecy last September. I went in that direction as I went to Carcassonne after Annecy and the train out of Annecy made more sense than Chamonix.

I did 3 nights in Cham and 2 in Annecy and I'm not at all a hiker (and am afraid of heights so almost hyperventilated when I got to the top of the Aguille du Midi) but I would absolutely do it the same way again. Both Chamonix and Annecy are very tiny and walkable. Although from the bus station in Chamonix to most hotels is a little bit of a walk, depending on where you stay.

Yes, Annecy is still crowded. I’m with a group that visited Chateau Menthon St Bernard above Annecy today. There was a lot of traffic and our guide said Annecy was still crowded.

Near the lake, it’s really quite urban for someone who wants villages and nature. You’ll need to check bus connections.

We took a trip to France last year that sounds a little like yours. We landed at the Geneva airport and took a BlaBlaCar bus to Chamonix on Sept 1. Expect heavy traffic when leaving Geneva, but hey you're not driving! When we arrived in Chamonix it was raining hard, but this was the only rain we had on this part of the trip. I would definitely book at least three nights, as the Aiguille Du Midi Gondola is a must-see, but Aiguille Midi/Mt Blanc is often buried in thick low clouds, in fact this was the case for the first day we were there. Next day was clear, but I was late (6pm?) to book the advance tickets on my phone, so our gondola ticket was not until about noon. Don't book the ticket if it will not be clear at the top. So, two days minimum in Chamonix and probably more if you arrive in late Sept. We took the cogwheel on the 1st day which was below the clouds and also spent a good time in Chamonix itself. We did not do much hiking. The following day, we took the BlaBlaCar Bus to Annecy. As I remember, the train connections to Annecy took a lot longer than the bus.
We did not stay at Dupalais (Hotel du Palais de l'Isle Annecy?) hotel mentioned, but the location seems good. At the most I would only spend 2 nights in Annecy, unless you are planning to travel to another lake town for a day trip, such as Château de Menthon-Saint-Bernard, for example.
-Bruce

We just returned from a trip to France. Flew into Geneva, arranged a private transfer to Chamonix, then took a bus to Annecy and finally a train to Paris.

I would schedule 3 days in Chamonix, only because going up to the Aguille du Midi is sooooo worth it but completely weather dependent. Chamonix is a nice enough town but the highlight was definitely the Aguille du Midi. You might also want to take the train to see what's left of the Mer de Glace glacier. It is rapidly receding due to climate change.

As for Annecy, the lake is beautiful (you can rent a bike or a paddle boat and spend a few house doing that) but to me, the Old Town was gimmicky and full of terrible food and tons of people. I really think Annecy is skippable. There were three of us and we all agreed Annecy isn't worth the hype. We did love Paris though.

both places could still be busy but less than July and August!
Check that you are not coming during the big UTMB race as crazy busy...
I will split my time between the 2 places and both are fine for solo travelers.
In Annecy, you could rent a bike and cycle around the lake, many hikes in the area...
In Chamonix, take the cable car to Aiguille, hikes, QC spa...
for more info on Annecy and things to do check my blog https://www.taxi-massingy.com/en/blog-en/

Not just the UTMB: if you are going to either area in September 2027 there is a 3 week long UCI "Super" World Championship cycling event. While it's headquartered in Sallanches, there are events in Chamonix, Annecy, and many other towns.

Speaking on cycling: one of the best ways to explore around Annecy is on a bicycle! There's a lovely multi-use path around the lake (with two legitimate climbs on the north side of the lake, caveat emptor if you aren't comfortable climbing). If you simply do an out-and-back on the south shore it's pretty much flat, separated from traffic, and has many cafés (and a few beaches) to stop at along the way. A bicycle will have you far from the crowds within minutes, and without any traffic issues. There are many shops that will rent bicycles by the hour or day.

I can also vouch for the Hotel du Palais de l'Isle Annecy - it's lovely! And they accommodated my personal bicycle with ease in their storage room. The location in the heart of the old town, which is a great place to wander (even with the crowds).

The UTMB is over. It started the day we left Chamonix.

I agree with you about Annecy, pjmun.
Edit: I spent all day today in Annecy again with a French group on a historical tour. Still not my favorite. But the architecture is amazing in the old town if you keep your eyes above the Disney ground floor where all the tourist businesses are. I’d give it 24 hours to appreciate the 16th-18th Century architecture. It’s a very urban setting and locals are fed up with the over tourism.
Chamonix is Alpine, totally different, different culture, much higher altitude and alpine buildings. It fits your description better. I’m staying in an Alpine village with this group and much prefer it. It’s a few degrees cooler up in the Alpine areas.

Hello again,
Thank you so much to everyone for all the valuable advice and tips! I really appreciate you taking the time to help me out. I will definitely take all of your comments into consideration while planning my trip. (Aiguille du Midi looks a bit hard for me , so I can try lower alternatives:)
It seems that Annecy is still crowded, I will probably arrive on Saturday . Actually I was planning to start from Chamonix and then to Annecy but weekends hotel prices are expensive in Chamonix . As you already know the area, what would you recommend? First 1 day (or 2 days?) : Saturday in Annecy and 2.day afternoon Chamonix . Last day chamonix to geneva . Or should I do vice versa? Thanks again

If it’s this coming weekend, Annecy has no rain forecast, while Chamonix has 40% chance during the day on Friday. This can change but our stay this past week had better weather than predicted. So, I’d base the stays on the weather and go to Annecy first.

if you are not doing the cable car ride and weather is unsure, I would skip Chamonix...
You could get to Col des Aravis, La Clusaz, Grand Bornand (all near Annecy) to get mountain air and maybe view on Mont Blanc...