We followed the advice of davidzet, and did our own DIY day tour from Latacunga. With a little research, you can find buses from the main bus station in Latacunga for a few dollars each, each way. The journey takes about 60-90 minutes each way.
You either want to get a bus directly to Quilotoa (less frequent), or a bus that goes to Quevedo and get off in Zumbahua (more frequent), then get a taxi/combi up to Quilotoa.
Our bus up was pretty shabby, and they pack the locals in with no standing room left, quite an adventure. The bus back was more relaxed, but the scenery along the way is amazing.
The crater and lake are spectacular, and I could easily have spent a lot longer there. We didn't hike to the bottom, other people have told me it is worth it, but a long hard slog back to the top.
There are a few restaurants and hotels in Quilotoa, but all looked very basic. We had a good, cheap almuerzo in one place opposite the crater viewing platform, but I developed gastroenteritis the next day, so pick carefully!
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