Two and a Half Days in Crete

Why did you book the ticket and THEN ask our advice? If you are talking about flight tickets, why not fly into Heraklion and then out of Chania??? If you are using the Aegean Air FLEX level of ticket, you should be able to change outbound flight from Heraklion to Chania. If you don't want to do that, I have no advice ... there is no "best sequence" for only a 48 hour stay.

After landing in Heraklion, find a place to store your luggage, visit Knossos and Archeological Museum. If you can do all of that on your arrival day in Heraklion, then stay both nights in Chania, a beautiful historic small city, Venetian Harbor. Try to fly out of Chania if you can change your tickets. With such a short time, don’t rent a car as you will enjoy staying in Chania the whole time.
Crete is very large,160 miles long; we spent two weeks and barely scratched the surface. You will want to return.

Dining in Chania- Well of the Turk and Tamam are both excellent.

There is a bus stop just across the street from the Archeological museum in Heraklio, that will take you to Knossos. The bus stops in the Knossos parking lot very close to the ticket booth.

Rome2Rio is a great site for planning transfers:
https://www.rome2rio.com/map/Chatzidaki-1-Iraklio-712-02-Greece/Knos%C3%B3s

From the link above you can see how close the bus stop is to the museum. If you click on the taxi icon you can see where a taxi stand is located a couple of blocks away. If you're short on time, perhaps you want to take a taxi instead.

Two nights means one day to explore, although your early arrival and late departure gives you a little extra time.

We arrived by fast ferry in Heraklion, spent the night, and visited the Palace of Knossos and the Archeological Museum in one day. Note that these two sites are not close to each other. The Palace is out of town. We walked to the bus stop from our hotel and took a bus to it. The museum is in town, close to where we got that bus and where it dropped us off.

We stayed at the Lato Boutique Hotel, on the water and close to the ferry dock. It's very modern with a nice restaurant upstairs with good views and a lovely one downstairs where a super buffet breakfast is served.

We went on to Chania by bus. It left from the port, just down the hill from our hotel. That was fun, but it took about 3 hours. We spent 3 nights there and took an overnight ferry to Piraeus. I really don't think you have time to go to Chania and return to Heraklion. I'd stick to what there is to see in or near Heraklion.

Crete Travel has links to information about transportation on the island, as well as to lots of other useful information on Crete.

A quick little Google search on churches in heraklion crete produced these results.

Thank you all for your suggestions. The decision to pass by Crete came as an after-thought, so I had rushed to insert it in my travel itinerary. As Janet said, I should have asked first before finalizing my flight schedule. Now I have two options and I hope I would be able to get additional tips on both possibilities:

1. I will try to change my exit airport to Chania from HER. I did not know that Chania has also an airport that offers connection to other countries (outside of Greece), or perhaps I could connect to international airlines by flying back to Athens from there.) If I could do this, then I trust I could accomplish my original Crete itinerary. Yes?

2. The other options, as also suggested by some of you, is to just concentrate the sightseeing around Heraklion. Are there other suggestions of what to see, in addition to the Archeological museum and Knossos?

Thanks again,

CP

You can connect to other airlines by returning to Athens from Chania. If there is a slight fee involved in changing airports... remember that in so doing, you will save the cost of going to Chania & back (along with the time saved) You did not share what was your next step beyond flying out of Heraklion. It is so hard to advise when given very incomplete info.... i.e. what your RT flight route to/from Greece is... nonstop from US or what? Sigh. Good luck.

Are you prepared to rent a car and drive into the surrounding area? If so, you might head east to the beautiful area around Agios Nikolaos and visit the island of Spinalonga with its evocative Venetian fortress which was later occupied by the Ottomans and then became a leper colony, finally closing in 1953. If you choose to do this you might want to pick up a copy of a book by Victoria Hislop called The Island. It is a highly romanticized novel about a woman who contacts the disease and is sent to the colony in the early 20th century until it’s closing. But it does give a sense of the fear the disease caused and how lepers were ostracized until a cure was found after WWII. I imagine there are companies in Heraklion that offer tours out to the area as well. It would be a full day trip.

Ianlubber, OP already has specifically expressed priorities of seeing Knossos, Architectural Meseum (those will take a full day) and a walkking tour of Chania. They cannot possibly fit in a long journey to Spinalonga, attractive as it may be. That is for another trip.

If you can't change your itinerary, from the Heraklio area perhaps you want to day trip to area sights. With a car you could venture west to the northern Amari Valley with church frescoes, Moni Arkadiou and the Eleftherna museum. You could visit Rethymno, which we did not visit (due to time constraints) but sounds like it has a charming city center. All of the previous would give you a taste of the more recent history of Crete, provide a variety of landscapes, and I think are doable in a day. You could also day trip south to Phaestos, Gortyna, and sights in the Messara valley area. That feels like a fairly long daytrip so perhaps not as good. We liked Heraklio, but after one and a half days we had seen everything we wanted to. The Viatour site for Heraklio has some ideas if you don't want to rent a car, and I'm sure there are other tour companies as well.