LAST UPDATED: 9/12/26 – Planning for Machu Picchu and Galápagos

After months of planning and organizing, our planning for Machu Picchu and the Galápagos Islands is finally complete.  We have been doing our best to take you along with us during our planning process so that we can demonstrate to you how our unique planning process works.  Hopefully, this information has been helpful for you, and you will be able to use some of this process to plan your future trips.

During Part 1 of our planning for the Machu Picchu and Galápagos series, we discussed the What, Where, and When of our planning process.  We showed you how we typically determine when it would be best to visit a specific location by looking at the average temperatures, precipitation levels, and tourist numbers throughout the year.

For Part 2 of the planning for the Machu Picchu and Galápagos series, we focused more on the How and the How Long by looking at how it would be best to visit these areas.  We took a look at the Tour Package, the Solo Planning, and the Combination approaches to planning a trip.

In this final segment of our planning for the Machu Picchu and Galápagos process, we are going to finish answering the question of how. It’s relevant as it pertains to our transportation options and accommodations. In Part 2, we were able to outline a rough itinerary of our trip, and in this article, we are going to fill in the blanks. The good news is that this will ultimately allow us to answer the final question in our planning process: the How Much.

Rough Itinerary Review

Before we get into the planning of our transportation and accommodations, let’s review the rough itinerary that we outlined in Part 2 of our planning process. As you can see below, we are set to fly to Lima, Peru, on Monday, September 3, 2018, and return from Quito, Ecuador, on Friday, September 15, 2018.

Booking Flights

You can also see on the itinerary that we have several travel dates for which we have to fill in transportation.  These dates are as follows:

• On September 5, we need to get from Lima, Peru, to Cusco, Peru
• On September 7-8, we need to get from Cusco to Baltra, Galápagos
• On September 14, we need to get from Baltra to Quito, Ecuador, to fly home

At first glance, this may not look too difficult. We only have 3 travel dates that we need to take care of, so booking airfare should be a breeze. In reality, it wasn’t all that simple. We are flying from some small airports in isolated locations, so the number of flight options isn’t as great as it would be if we were flying from major cities.

We also want to make sure we build some buffer time into our travel so that we have some flexibility to overcome a delayed or cancelled flight without missing our scheduled tours. In the end, this required quite a bit of thought and planning, but I think we have a pretty solid plan.

Flight from Lima, Peru to Cusco, Peru

For the flight from Lima to Cusco, there wasn’t as pressing a need to build in flexibility, as we aren’t scheduled to begin our tour of Machu Picchu until September 6. However, we are planning on spending September 5 in the Sacred Valley to assist in acclimating to the altitude, so we wanted to make sure we got an early flight to Cusco.

We booked an early‑morning flight to Cusco on September 5. These days, fares on this route typically range from $150–$250 per person, depending on demand and season.

Flight from Cusco, Peru, to Baltra in the Galápagos

Planning our transportation from Cusco to the Galápagos turned out to be more complicated than expected. We needed to reach Baltra before noon on September 8, but there are no direct flights from Cusco to Baltra.

LATAM and Avianca both operate regular Galápagos‑bound flights, but all departures still leave from Quito (UIO) or Guayaquil (GYE) — never from Cusco or Lima. While schedules have improved somewhat these days, tight morning arrival windows remain, and travelers still need to plan around early departures and the possibility of delays.

Once we started looking at connections through those hubs, the logistics became even trickier. Many itineraries were twenty‑nine hours or longer, often involving overnight airport stays — something we try to avoid when traveling. Long layovers also meant spending far more time in transit than necessary, which didn’t fit well with the rest of our plans.

These days, itineraries from Cusco to Baltra are generally 12–18 hours, depending on the routing. Overnight airport stays are no longer typical, but overnight city stays are still recommended because Galápagos flights depart early and delays on domestic Peruvian routes remain common.

Timing was the biggest challenge. Several flights left Cusco on September 7 but didn’t reach Baltra until late morning or afternoon on September 8, leaving almost no buffer if a delay or cancellation occurred. With such a tight arrival window before our tour, we needed an option that offered more reliability and flexibility.

Building in Flexibility is Important

In Tanzania, we had a flight from Arusha to Zanzibar cancelled on us multiple times, so we know first-hand the importance of building some flexibility into your flight schedules.

In the end, we ended up booking a flight out of Cusco early in the morning on September 7 that arrives in Quito early in the afternoon on September 7. Instead of sitting in an airport overnight, we are going to spend the night in a hotel in Quito on September 7. This will allow us to spend the day exploring Quito and not have to worry about dealing with a long layover.

On September 8, we will get up very early in the morning for a flight from Quito to Baltra. We are going to catch the earliest flight to the Galápagos; that way we have options for catching a later flight should our flight get delayed or cancelled.

To further validate our choice before booking, we took a look at the on-time history of this flight on flightstats.com to see how often this flight has been delayed or cancelled. With a 100% on-time history, we felt confident enough in our choices to book these flights. Combined, these flights cost us approximately $550 per person, which isn’t bad.

NOTE: FlightStats no longer provides free public on‑time performance data for specific flights. Travelers now rely on Cirium, FlightAware, or airline‑published reliability metrics. No Galápagos‑bound route maintains a 100% on‑time record, and seasonal delays are common, especially during June–September.

Flight from Baltra to Quito

Our last in-trip flight that we had to book was a flight from Baltra to Quito on September 14 to catch a flight home. At this point, we hadn’t booked our flight home yet, so we had some options. Our Galápagos Islands tour wraps up in the early afternoon on September 13.

We could have looked for a flight home from Quito on the evening of September 13, but that would be really tough to do and build in some flight flexibility. The last thing we want to do is miss our flight home from Quito.

So, instead of pushing our luck, we decided to spend the night in Quito on September 13 and then book a flight home from Quito on September 14. This would give us plenty of flexibility should our flight from Baltra to Quito get delayed or cancelled, and it would also give us some more time to explore Quito. It’s a win-win. We ended up finding a flight for roughly $200 that was reasonable, which gets us to Quito in the early afternoon, so we are pretty happy about that.

Booking Hotels

In addition to flights, we also had to find accommodations for quite a few days. Our Galápagos tour takes care of our accommodations from September 8 through September 13, so we don’t need to worry about finding a place to stay on those nights. However, there are some nights when we have chosen to take care of accommodations on our own.

• On September 3-5, we need a hotel in Lima, Peru
• On September 5-7, we need a hotel in Cusco, Peru
• On September 7-8, we need a hotel in Quito, Ecuador
• On September 13-14, we need a hotel in Quito, Ecuador

Here is where saving up your hotel points really comes in handy. We have accumulated a large amount of Marriott points through our other travels, so we plan to use these points to save on hotel bookings as much as possible for these dates. In the end, we were lucky enough to book all of these dates at Marriott properties.

Hotel Accommodations in Lima for September 3-5

When we arrive in Lima on September 3, we are going to need hotel accommodations until we depart from Cusco on September 5. Lucky for us, there is a Marriott Courtyard Miraflores in Lima that we can use our hotel points to book. Thus, the cost for this hotel ended up being $0.

Hotel Accommodations in Cusco for September 5-7

We are flying from Lima to Cusco on September 5, so we need a place to stay in Cusco until we depart for Quito, Ecuador, on September 7. Again, we got lucky in that there is a Marriott property in Cusco. We were able to make a reservation at the JW Marriott El Convento Cusco for both nights, which we are very happy about.

We did look at possibly booking a night or two at the Belmond Sanctuary Lodge, which sits just outside the gates of Machu Picchu, but it was way outside our price range.

During the time we are visiting, the hotel so charging roughly $1,200 a night per room. It would have been very cool and convenient to stay right outside of Machu Picchu, but we just couldn’t justify that cost. Instead, we booked our stay at the Marriott for a total cost, with points, of $0.

NOTE: The days, the Belmond Sanctuary Lodge rates typically range from $1,600 to $2,200 per night, depending on season and room type. Demand has increased significantly, and the property remains one of the most expensive hotels in Peru.

Hotel Accommodations in Quito for September 7-8

The next night of accommodation that we needed to take care of was for the night of September 7, checking out the morning of September 8. As I mentioned earlier, this is the night that we will be spending in Quito on our way to the Galápagos instead of spending the night in an airport.

We were happy to discover that Marriott has a hotel in Quito. Instead of spending an uncomfortable night in an airport, we will be spending the day exploring Quito and then spending the night at the JW Marriott Hotel Quito. With points, the cost will be $0.

Hotel Accommodations in Quito for September 13-14

The last night that we needed to worry about finding accommodations for was our final night of the trip. Remember, instead of opting to try and find a flight home from Quito on September 13 when our Galápagos tour is finished, we are building some flexibility into our flight schedule and not flying home from Quito until September 14.

Lucky for us, we already know that there is a Marriott property in Quito for us to take advantage of, so we booked a night at the JW Marriott Hotel in Quito for the night of September 13 with Marriott points. Again, with points, the cost was $0.

Flights to Lima and Home from Quito

The last logistical task we had to sort out was our main flights to Lima and then home from Quito. In addition to Marriott points, we have also accumulated several Delta Airlines miles that we can take advantage of.

We ended up finding a Delta Airlines flight that departs in the late evening of September 3, arriving in Lima, with a return flight from Quito that gets us home in the early afternoon on September 14. With points, including taxes and fees, the tickets will cost us approximately 81,000 points and $106 per person.

Comparing the Cost of This Trip to Full Tours

As we mentioned in Part 2 of our Machu Picchu and Galápagos Islands planning, we decided to use a combination of self-planning and destination tours to travel to Machu Picchu and the Galápagos Islands. We call this the combination option. The reasons we prefer to use this option when traveling are the flexibility and moderate cost savings this option provides.

While this way of planning a trip doesn’t afford the flexibility and cost savings that planning your entire trip on your own does, it does afford quite a bit more flexibility and cost savings than taking a full-blown tour does. As a reminder, here are some of the full tours that cover both Machu Picchu and the Galápagos Islands that we were able to find.

Please Note: These prices may change, so please be sure to check the websites for the current pricing.

• Vaya Adventures – $9,650\person (not including flights)
• SA Expeditions – $7,790\person (not including flights)
• Collette – $10,299\person (not including flights)
• Smithsonian Journeys – $11,493\person (not including flights)

By taking care of some of our transportation and accommodations, but using tours to see Machu Picchu and the Galápagos, we still get the advantages that go along with using a tour to see a destination, but we saved quite a bit of money relative to using a full-blown tour. Here is a breakdown of the costs of our trip. This is the total cost for all flights, all hotels, all tours, and all extra costs for visiting Machu Picchu and the Galápagos.

Total Trip Cost Breakdown:

NOTE: Domestic and regional airfare in Peru and Ecuador has increased since 2018. Typical pricing today is:

• Lima → Cusco: $180–$260
• Cusco → Quito (via Lima): $350–$500
• Quito → Baltra: $320–$420
• Baltra → Quito: $280–$380

With today’s pricing, the same itinerary—assuming identical use of points—would cost closer to $3,200–$3,800 per person, primarily due to increased airfare and hotel rates. Travelers paying cash for hotels would see totals in the $4,300–$5,300 range.

Granted, we are saving quite a bit of money by using hotel points and airline miles. However, even with the full tours, most tour costs do not include the cost of flights.

We like to pay for our flights on cheaper trips, even if we have the miles to use, so that we can cut costs on bigger trips like this. Flights are such a big piece of the cost of a trip, and it helps significantly if you can cut that price out of the equation.

The same thing applies to hotels. We like to pay for our hotels on smaller trips, even if we have the points to use, because it allows us to further cut costs on these big trips.

If we paid for our hotels on this trip, at $150 a night, it would add up to an additional $900 in cost. That would put the total cost of our trip per person at $3,432. That is still significantly below the cost of a full tour that visits both Machu Picchu and the Galápagos Islands.

NOTE: Hotel prices in Lima, Cusco, and Quito have risen since 2018. Mid‑range hotels now average $180–$250 per night, meaning the same six nights would cost $1,080–$1,500 instead of $900.

With this, we have answered the final question in our trip planning process. We now know How Much it will cost us to take the trip. Should the cost be too high when doing planning for your trip, you can go back and make adjustments before booking your tours, accommodations, or flights. With the information you have gathered in your planning, you will know which costs you can cut that will have the biggest impact on the bottom line for your trip.

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