People come to us with the three legs already picked: islands, Andes, jungle. What's left is one real question: what do you do first? The answer isn't taste, it's altitude. Here's the order that keeps you feeling well enough to enjoy all three.
Sequence by altitude, not taste. The Galapagos sits at sea level, the Ecuadorian Amazon near 300 m, Quito at 2,850 m, and Cusco at 3,400 m — so the high Andes is the only leg your body has to prepare for. Give the Andes its own acclimatization days; the sea-level and jungle legs won't build tolerance for you. A common 16–20-day order: Andes first (arrive Quito, acclimatize), then the low Amazon, then the Galapagos to end on the water. Current departures and starting prices for the Galapagos leg are in the table below. Ask your doctor about altitude medication before you travel.
You've got three ecosystems and a fixed number of days, and the instinct is to sequence them by whatever excites you most: dive into the islands first, save the jungle for later, fit the mountains in wherever they land. That instinct is the wrong variable. The one thing that actually decides the order is elevation, because only one of these three legs carries an acclimatization cost.
Ecuador is the country that makes this trip possible without ever leaving one border: Quito and the Andes highlands inland, the Amazon lowland to the east, the Galapagos Islands offshore. Add Peru's Cusco and Machu Picchu and you're extending the same logic higher, not changing it. Either way, the question isn't which leg you want most. It's which leg needs a runway of days before you go higher, and which don't.
Here's where each leg actually sits. The Galapagos Islands are at sea level, full stop. The Ecuadorian Amazon (the Coca, Napo, and Yasuní region most Amazon trips fly into) sits around 250 to 400 meters, still functionally low. Quito, where an Ecuador-based Andes leg starts, is at 2,850 meters. If the trip extends into Peru, Cusco sits at 3,400 meters, with the lower Sacred Valley near Urubamba, about 2,870 meters, as the step most travelers use to acclimatize before going higher.
| Leg | Elevation | Acclimatization needed? |
|---|---|---|
| Galapagos Islands | Sea level | No — altitude-neutral |
| Ecuadorian Amazon (Coca / Napo / Yasuní) | ~250–400 m | No — altitude-neutral |
| Quito | 2,850 m | Yes — plan the route around this leg |
| Sacred Valley / Urubamba (Peru, if included) | ~2,870 m | Used as the acclimatization step before Cusco |
| Cusco (Peru, if included) | 3,400 m | Yes — ascend gradually |
The rule that actually matters: altitude sickness risk rises with how high you go and how fast you get there, not with fitness level or age alone. And time at sea level or in the lowlands doesn't pre-acclimatize you for anything higher; you only build tolerance by spending time at moderate altitude before you go higher still. That's why the Galapagos and the Amazon count as altitude-neutral legs here. Neither helps you get ready for the mountains, and neither hurts you. The Andes is the one leg that needs its own days built in.
A note on altitude and health: this is general guidance, not medical advice. Talk to your doctor about altitude medication, such as acetazolamide, and about your own risk factors before you travel.
"The idea I correct most is that a few days at sea level get you ready for altitude. They do not. Sea level does not build any tolerance — if anything you arrive at Quito or Cusco having lost whatever you had. Altitude is the only leg your body actually needs to prepare for, so it gets its own acclimatisation days at the start, and the sea-level legs go around it. Plan it the other way and you spend your first day in the Andes with a headache."
— Evelyn Duran, Co-Owner
Start in the Andes. Arrive in Quito at 2,850 meters and let your acclimatization days happen at the front of the trip, while you're fresh off the flight rather than tired from two other legs already behind you. If the itinerary climbs further, to Cusco at 3,400 meters, ascend gradually and build in Sacred Valley days rather than jumping straight from Quito to Cusco in one hop.
From there, drop to the low Amazon. It's a rest for the body, not a climb: no altitude to manage, no acclimatization clock running, just the jungle at its own pace.
End at the Galapagos. Sea level, with zero altitude concern left to plan around, so the trip closes on the water rather than opening there.
Why not the islands first? It's tempting, and we hear the request often. But putting the islands first pushes the one leg with an acclimatization cost, the Andes, to the tired end of a long trip, and gives your body no elevation runway before you ascend. That's the order working against you instead of for you.
When we flip it: island cruise availability and cabin dates can force the Galapagos to the front of a route, and so can a regional flight schedule or the choice between an Ecuador-only trip and an Ecuador-plus-Peru one. If the Galapagos has to go first for your dates, the fix isn't to skip the acclimatization days when you reach the Andes afterward. It's to add them anyway.
"In most cases, I recommend starting with Machu Picchu and finishing the trip in the Galapagos. After touring cities, archaeological sites, and several transfers, the Galapagos offers a much more relaxed ending, focused on nature and wildlife. Also, after walking at altitude in Cusco and the Sacred Valley, many travelers are grateful to finish their vacation at a calmer pace, enjoying the sea and the archipelago's unique wildlife."
— Marcelo Guerrero, Co-Owner
Here's how the order above plays out as an actual route, leg by leg, with elevation next to each stop so you can see the shape of it: up into the Andes, level off in the Amazon, down to sea level in the islands.
Arrive in Quito (UIO), 2,850 meters, and spend your first days at that altitude before going anywhere higher. If Peru is part of the trip, fly on to Cusco (CUZ), 3,400 meters, and acclimatize in the lower Sacred Valley, about 2,870 meters, before Machu Picchu, which runs on timed-entry tickets, a licensed guide, and a fixed circuit rather than a walk-up visit. The Galapagos and Ecuador legs are ours: we build, book and run them. Beyond Ecuador we work with established operators on the ground, and like any tour operator we don't publish who they are. What we will do is sequence the whole trip so the flights and the pacing work, and tell you plainly which parts we control and which we don't.
From the Andes, return to Ecuador and drop to the Amazon: fly Quito to Coca, then a river transfer to a lowland lodge around 300 meters. No altitude to manage here, just the jungle. The Ecuadorian Amazon is our own product, so we pick the lodge and the region to match your dates and how far you want to be from the airstrip.
Finish in the Galapagos: fly Quito or Guayaquil to Baltra (GPS) or San Cristóbal (SCY), sea level, for a cruise or a land-based stay. The vessel, itinerary, and price-from for your dates are quoted live rather than printed here as a stale figure.
Two ways to run this:
The Ecuador-only route — the cleanest acclimatization profile. Andes, Amazon, Galapagos, all inside Ecuador, no second country, and a top elevation of Quito's 2,850 meters rather than Cusco's 3,400. Typically 12 to 16 days.
The Ecuador-plus-Peru route. Adds Cusco and Machu Picchu on top of the same Ecuador legs, typically stretching the trip to 16 to 20 days total. If a longer version of this appeals more than the compact one, our South America in three weeks guide walks through the extended build.
Altitude decides the skeleton of the order. Weather and logistics decide the finer points.
The Galapagos runs year-round: warmer, wetter months from December to May, cooler and drier from June to November. The Ecuadorian Amazon is wet for much of the year, with higher water levels from March to July that help canoe access into parts of the forest, and drier trails from August to February. If Peru is in the trip, Machu Picchu's dry season runs May to September, and the Inca Trail closes every February for maintenance. Line the three windows up and June through September is where all three legs sit at their easiest.
The logistics reality is plainer: everything routes through the mainland hubs, Quito (UIO) or Guayaquil (GYE). There's no direct flight between the Galapagos and the Amazon, and none between the Galapagos and Peru, so every transition between legs costs a mainland connection and often an overnight in Quito. The regional carriers are Avianca and LATAM. Factor in the $200 Galapagos National Park entry fee and the $20 INGALA transit control card for the islands leg, on top of whatever Peru or Amazon entry costs apply to your route.
For how the days add up across a full Ecuador itinerary, see our how many days to visit Ecuador guide, and for the jungle leg itself, our Amazon rainforest and jungle tours page.
Ecuador holds all three ecosystems inside one border: the Andes at Quito's 2,850 meters, the Amazon lowland around 300 meters to the east, and the Galapagos Islands offshore. That makes the whole three-ecosystem trip bookable without a second country, and with a gentler top elevation than a route that climbs to Cusco's 3,400 meters. We treat that as the strength it is, not as a downsell of the Peru extension.
Beyond the islands, the two mainland trips we sell most are Amazon rainforest tours and Andes highlands tours — which happen to be exactly the two legs this route needs. That's not a coincidence. It's the same three-ecosystem logic our own booking pattern already reflects.
For families with children under 6, most Galapagos cruises don't accept guests that young, and a land-based Galapagos stay pairs naturally with an Andes-and-Amazon mainland trip. Treat that as a feature of the route, not a workaround.
Our Galapagos and Machu Picchu hub covers the two-country combinations in more depth, including how the Peru extension changes the sequencing math above. For the Ecuador-only Amazon pairing specifically, see Galapagos and the Amazon.
Talk with an expert insider — we'll sequence your Galapagos, Andes & Amazon route in 24 hours.
USA & Canada 1-773-280-9571 · Ecuador +593-987-004-404 · [email protected]
Start in the Andes so your acclimatization days happen early, while you're fresh. Drop to the low Amazon next, since it carries no altitude cost and works as a rest between the mountains and the islands. Finish in the Galapagos at sea level, so the trip closes on the water with nothing left to acclimatize for. Flip the order only when cruise dates or flight schedules force it, and add the Andes acclimatization days wherever they land instead of skipping them.
Either works, because the Amazon carries no altitude cost in either direction. What we usually recommend is Amazon after the Andes: acclimatize in Quito or the Sacred Valley first, then use the lowland jungle as a rest before or after the highest point of the trip. Doing the Amazon first doesn't hurt you either, since low elevation never pre-acclimatizes you for what comes next.
Yes, if the Andes come next. Time at the sea-level Galapagos doesn't build any tolerance for Quito's 2,850 meters or Cusco's 3,400, because acclimatization only comes from time spent at moderate altitude, not from time at low elevation. If your route puts the islands before the mountains, plan acclimatization days in the Andes exactly as you would if you'd flown there directly.
No. Both sit at low elevation, sea level for the Galapagos and roughly 250 to 400 meters for the Amazon, and neither builds tolerance for altitude. Acclimatization only happens by spending time at moderate elevation before you go higher, which is why we treat both legs as altitude-neutral rather than as preparation for the mountains.
A common range is 16 to 20 days for all three, including the Andes acclimatization days, a few nights in the Amazon lowland, and a Galapagos cruise or land-based stay. An Ecuador-only version, without Peru, can run tighter, often 12 to 16 days, since the top elevation is Quito rather than Cusco. Add extra days if Machu Picchu is part of the route.
Yes. Ecuador holds all three: the Andes at Quito's 2,850 meters, the Amazon lowland to the east around 300 meters, and the Galapagos Islands offshore. That's the whole three-ecosystem trip inside one country, with a gentler top elevation than a route that extends into Peru's higher Cusco and Machu Picchu.
Yes, on the Andes leg specifically, not the Galapagos. Risk rises with how high you go and how fast you ascend, not with fitness or age alone. Quito sits at 2,850 meters and Cusco at 3,400, so build in acclimatization days rather than flying straight to altitude and starting activities the same day. Ask your doctor about altitude medication, such as acetazolamide, and your own risk factors before you travel.
Live availability and starting prices for our Galapagos departures. Dates and rates update automatically.
Tell us your rough dates and whether Peru is part of the picture, and we'll come back within 24 hours with an order built around your itinerary: the acclimatization days placed where they actually help, the mainland connections mapped out, and the Galapagos leg priced for your dates.
USA & Canada 1-773-280-9571 · Ecuador +593-987-004-404 · [email protected]
Start with our hub, Galapagos and Machu Picchu itinerary, or see the two related routes: Galapagos and the Amazon and South America in three weeks.
