Incas & the Amazon: 2-3 week Peru travel itinerary from Lima to Manu National Park

December 14, 2019

Thanks to Peru’s rich history and incredible diversity, it’s possible to journey from a bustling metropolitan city on the Pacific Coast, through Cusco’s cobbled lanes, along a high-alpine trail to an ancient Incan citadel in the mountains, and then wind-down in an untouched stretch of Amazon Rainforest, all in under 3 weeks. It’s actually far from everything the country has to offer (after 2 months, I still haven’t gotten enough of this magical place), but it’s an undeniably impressive highlight reel that will inspire countless future visits to Latin America and vibrant Peru. This itinerary includes everything you need to know about planning a trip to Peru, sampling world-renowned cuisine, watching the sunrise from Machu Picchu, and napping in hammocks with wild monkeys.

Check out my other Peru travel itineraries or my detailed Peru travel guide for heaps more information about planning the best trip to Peru:

What's in this travel guide

Planning for your trip

Best time to go

Peru is a phenomenal year-round destination, but there are definitely certain times better for visiting Lima, Machu Picchu, and the Amazon. Lima is at its sunniest and most beautiful in the winter (December – February), whereas the Amazon is cooler and drier from around May – October (temps can still get up into the 30s).

Cusco and Machu Picchu are also decidedly more enjoyable from June – August. If the very start/end of the year is your only time to travel, though, you can still have a wonderful trip— I spent a month in Peru in December and loved every wet minute— but the clear sunrise at Machu Picchu and the blue skies in Cusco during my August visit were undoubtedly more picturesque.

Perfect weather in the mountains in August

Getting to Peru

For this itinerary (and 99% of all Peru trips), you will fly into Lima through the Jorge Chávez International Airport, situated just 10km (20-30min drive) from the city centre or 18km (40-60min drive) from the popular tourist districts of Miraflores and Barranco. The best way to get to your hostel is with the Airport Express bus; book your ticket in advance online for $8USD or at the counter in Arrivals (next to the car hire companies, right before customs).

Depending on where you’re flying from, you might have a layover in Santiago or Buenos Aires, but Lima is a major hub for Latin America, so flights are typically reasonably priced and fairly direct these days.

When I flew to Lima from Sydney in 2014, it cost $2,300AUD and involved 4 flights, but when I flew in 2019, it was just $1,200AUD and included only a single stopover in Chile! There are so many routes from Australia, New Zealand, Europe, and America now that prices are far cheaper than they used to be. From the US, flights can actually be as little as $500USD return.

Getting around Peru

Peru actually has one of the best networks of public buses I’ve seen anywhere in the world. All main cities have large bus stations (sometimes several) that service heaps of near and far destinations around the country, buses constantly running throughout the day and night, and dozens of competing companies.

RedBus is my favourite site for checking bus times and routes in advance and I’d also suggest reading this post for heaps of info about booking bus tickets in Peru.

You’ll need to fly between Lima and Cusco (the 24hr bus ride through the Andes is quite literally torture and I would never, ever recommend it), so look for an inexpensive flight with Latam, Viva Air, Peruvian, or Sky. Other than this, you can get anywhere you need to go on a bus!

Health & safety concerns

It’s impossible to say that any destination is “completely safe”, but Peru would have to be fairly close— I was totally comfortable travelling by myself throughout the country and, taking basic safety precautions, didn’t really feel uncomfortable once. As long as you can speak some Spanish, it’s incredibly easy to get around and the locals are amazingly friendly, always willing to help.

With this particular Peru itinerary, there is a small risk of malaria and yellow fever, specifically in the Amazon. You can mitigate most of the risk with bug spray, but if you want to be extra cautious, you can also buy a malaria prophylaxis and get vaccinated against yellow fever from a travel doctor before your trip.

The altitude in Cusco (3,400m) and along the Salkantay Trek (4,650m) will also be an issue for some, contributing to headaches, lightheadedness, fatigue, and possibly even altitude sickness. This itinerary is designed to help you acclimatise slowly and therefore minimise the risk of developing altitude sickness, but it’s still possible you’ll experience minor to moderate symptoms. I’d recommend checking out my post about altitude so you know what to expect, both in Cusco and on the Salkantay Trek.

Budget for Peru

There is a bit of variability with this itinerary, depending on how you want to travel around, what hostels you want to stay in, and what tours you want to join. To give you a good idea of what it costs, I’ve fully priced two options, a “mid-range” and a “shoe-string”. Both options include a 4-day Salkantay Trek tour and a 7-day volunteer stay at Chontachaka Ecological Reserve for $400USD, but I’d encourage you to fundraise for the volunteer project to help offset some of the costs!

The mid-range version of this itinerary is still for backpackers, but includes some nicer hostels or private rooms, flights to Cusco, and heaps of activities in Lima, Cusco, and the Sacred Valley. Peru is an inexpensive destination, so even at this upper end, you can do this full itinerary from Lima to Cusco for S/4160, or $100AUD per day.

For those on an absolute shoe-string backpacking budget who want to find the absolute cheapest accommodation, travel exclusively by public bus, skip some of the pricey tours, and fundraise half the cost of a volunteer project in the jungle, you can do this entire itinerary for only S/2380, or $57AUD per day.

Note that the table below only shows 8 days of food and accomodation because everything is included in the price of a Salkantay Trek tour (4 days) and in volunteering at Chontachaka Lodge (7 days; it has its own row on the bottom of the table).

Table showing budget for Peru travel itinerary Lima Cusco to Amazon Jungle

Essential packing list

4x shirts and singlets for warmer afternoons and hiking
Lightweight long-sleeve shirt for the Amazon
Fleece (only bring one, because you will definitely buy alpaca jumpers in Cusco)
Warm jacket (I’d recommend at least one down jacket because it gets crazy cold on the Salkantay Trek and in Cusco at night)
Rain jacket
2x tights or other comfortable pants
2x shorts for hiking and around town
Sunnies + hat
Sandals
Comfortable shoes for walking around (runners or converse)
Sturdy hiking boots + wool socks
Trekking poles (also possible to purchase in Cusco or hire from the trekking company)
25-35L day pack
Warm hat + gloves (can also purchase in Cusco)
Sunscreen + tropical-strength bugspray
Biodegradable hygiene products (don’t take normal toothpaste or shampoo to the Amazon, it’s super bad for the environment and most lodges won’t even allow it on the premises)
Passport (+ colour photo copies), credit cards
Phone with local SIM card (I’d recommend Bitel or Claro)
Books/kindle for lots of quiet afternoons in the Amazon
Camera + spare batteries!

The road to the Amazon

*Overview: recommended itinerary

Lima (2-3 days)
Cusco (3-4 days)
Sacred Valley (1-2 days)
Salkantay Trek to Machu Picchu (3-5 days)
Manu National Park (3-7 days)

Busy streets in downtown Lima

Huacachina oasis

Lima

Begin your Peru trip in Lima la gris, Peru’s notoriously grey and oft-overlooked capital city— but don’t think there’s nothing to see here! Although you won’t find Cusco’s colonial charm and it’s pretty rare to get a “beach day” even if the city is right on the Pacific Ocean, Lima is truly the culinary epicentre of Peru, making for the perfect introduction to all the delicious local cuisine you’ll be enjoying over the next few weeks. Sample flavourful dishes at one of the world’s best restaurants, Central, or learn to prepare ceviche yourself by joining a Peruvian cooking class.

Spend most of your time hanging out in Miraflores, a cool coastal neighbourhood with heaps of parks, great ocean views, and plenty of delicious things to do (it’s all about the food, people), but make sure you also venture into the chaotic city centre. Downtown Lima is dirtier, busier, and far less safe than the coast, but it’s exactly this loud and colourful insanity that will make your visit so fun. With a couple days in Lima, you’ll also have ample opportunity to embark on a day trip to either Paracas or Huacachina, both fabulous destinations within a couple hours of the capital. Peru Hop offers really convenient and inclusive 1-day tours out to these spots, which you can check out here.

Recommended time: 2-3 days

Highlights: Incredible Peruvian cuisine in this foodie capital; Parque Kennedy and its resident cats; Huaca Pucllana ruins; trendy coastal neighbourhoods Miraflores and Barranco, with beautiful sites like Parque del Amor and the Miraflores Lighthouse; exciting day trips to Huacachina or Paracas

Getting there: Fly into Lima’s Jorge Chávez International Airport and then take the super convenient Airport Express bus all the way to Miraflores without hassling with a taxi or a public transport. Book your ticket in advance online for $8USD or at the counter in Arrivals (next to the car hire companies, right before customs).

Where to stay: Central Lima is incredibly hectic, and while it’s part of what makes the city so fun to explore, I would recommend staying outside of the pandemonium in trendier and safer (if more touristy) Miraflores of Barranco, both of which are on the coast. I love Hostel Kokopelli Miraflores (S/30 per bed).

Koricancha and the Iglesia

Puka Pukara ruins near Cusco

Rainbow Mountain

Cusco

Next up on your itinerary is, quite possibly, the best city in the entire world! Once considered the spiritual and political heart of the vast Inca empire, Cusco (meaning “centre of the universe” in Quechua) is still one of the most vibrant and historically significant cities in Latin America. Its close proximity to Machu Picchu and some of the country’s best high-altitude trekking have made this enchanting city the centrepiece of nearly every Peru itinerary, and it’s honestly impossible not to fall in love. With its intriguing mix of ancient Incan spiritualism, Spanish colonial architecture, and modern Andean culture, just walking down the lively, cobbled lanes of Cusco is like stepping through history.

I’ve spent over a month in and around Cusco, and I still feel like I’ve hardly scratched the surface of this incredible place. Get outdoors on some of the best high-altitude treks in the world like or Rainbow Mountain or the Ausangate Circuit, shop for alpaca souvenirs, learn about ancient Incan history, and enjoy every single second in magical Cusco. If time allows, it’s also super rewarding to get involved in local volunteer projects. As both a destination and a launch pad to other adventures, there is no better place than Cusco.

Recommended time: 3-4 days

Highlights: Charming blend of Incan and colonial Spanish architecture; incredible history and many significant sites; ruins just outside the city; lively San Pedro Market and countless artisan markets; an endless variety of day trips, like Rainbow Mountain; amazing trekking, like Salkantay, Ausangate Circuit, and Palccoyo.

Getting there: The 24hr bus ride from Lima to Cusco is quite honestly unbearable (the twisting roads, the altitude, the never-ending journey…), so you should look for an inexpensive flight with Latam, Viva Air, Peruvian, or Sky. Depending on how far in advance you book and the time of year, flights can be $30 up to $100+.

Where to stay: The very best areas to stay in Cusco are either San Blas or the Centro Histórico. My favourite hostel in Cusco is Kokopelli, which is slightly more expensive than other dorm rooms, but worth every sol. They offer pod-style dorm beds (S/50) that make it feel like you’re in a private room, a great free breakfast (or free packed lunch if you’re departing on an early morning tour), on-site tour booking, and a lively bar and restaurant with surprisingly reasonable prices.

Salineras de Maras

SkyLodge just behind me, anchored into the side of the mountain

Sacred Valley

Just north of Cusco in the shadow of the Peruvian Andes, the lush Urubamba Valley once formed the heart of the Incan empire and was an important agricultural area supplying food for the surrounding regions. Now, this approximately 100km-long valley is home to some of Peru’s most impressive ruins outside of Machu Picchu and is an essential inclusion on any Peru itinerary. Consider buying a full Boleto Turístico for access into a number of sites around Cusco and the Sacred Valley; the ticket is S/130 and valid for 10 days, purchased directly from any of the included sites (like Ollantaytambo and Pisac).

Depending on your interest, you can spend 1 action-packed day or even 2 full days exploring the Sacred Valley. Most people visit the Incan ruins in Moray and Ollantaytambo and shop at the markets in Pisac, but there are also some amazing adrenaline-filled activities that will give you a more unique look at this popular destination. Natura Vive operates via ferrata climbing and ziplining tours for S/275, taking you high over the Sacred Valley for an incredible condor’s view of the stunning landscape. Another awesome option is riding quad bikes out to the Salineras de Maras, an incredibly impressive collection of some 3,000 salt pans built up the side of a mountain. However you explore this region, you will leave with a deeper appreciation for the Incas and the beauty of the Valle Sagrado.

Recommended time: 1-2 days

Highlights: Incan ruins at Ollantaytambo, Pisac, and Moray; via ferrata climbing above the valley; quad biking to the Salineras de Maras; shopping for alpaca products at colourful local markets.

Getting there: There are a huge number of tours out to the Sacred Valley, the cheapest of which can be booked last-minute in Cusco (or online for a bit more money). If you want to embark solo, it’s also possible to catch a bus for S/3-4 to either Urubamba or Pisac.

Where to stay: If you’re adventuring into the Sacred Valley overnight, a good place to stay will be in the charming town of Ollantaytambo. If money allows, though, the absolute best accomodation in the Sacred Valley is in the Sky Lodge, a glass dome mounted into the side of a mountain that offers insane views of the landscape. Prices start at S/1385 (including via ferrata), but it promises to be an experience you will never forget.

Salkantay Pass

Clear skies and sunny weather at Machu Picchu

Salkantay Trek to Machu Picchu

There are a number of treks to Machu Picchu, the Inca Trail being the most popular, but arguably the most spectacular in terms of scenery is the Salkantay Trek. This hike takes its name from Salkantay Mountain, the highest peak in the Cusco region which held great spiritual significance for the ancient Incas, who believed that mountains and their resident Apu (spirits) were the link between Kay Pacha (the human realm) and Hanan Pacha (the upper realm). Towering Salkantay remains highly revered as a one of the most sacred Apu even today, and it’s impossible to deny its mysticism as you walk beneath towering peaks and sparkling glaciers,

The Salkantay Trek navigates 70km of trail from Mollepata to Aguas Calientes and is traditionally completed in 5 days. However, a number of modifications can be made to this trek thanks to nearby roads/trains, which effectively cuts out the penultimate day for a shortened 4-day trek or a challenging 3-day trek. Although at high altitude and with several steep ascents, this trek is manageable for most fit walkers and is an awesome way to approach magical Machu Picchu.

As mysterious as it is breathtaking, Machu Picchu is quite possibly the best preserved Incan archaeological site in all of South America, but certainly the most beloved. This is one of those rare places that actually exceeds all expectations, far more magical in person than even perfectly timed and heavily edited Instagram photos can convey. And even though it’s probably been on your mind since the first moment you contemplated a trip to Peru, experiencing it at the end of the Salkantay Trek is a dramatic, slow reveal that only magnifies the beauty.

Recommended time: 3-5 days

Highlights: Stunning alpine scenery over Salkantay Pass; incredible colours at Laguna Humantay; experience Machu Picchu at sunrise; climb Huayna Picchu for views over the ruins.

Getting there & away: Trekking tours depart Cusco and include return transport by way of train and shuttle back to town. It’s also possible to do the Salkantay Trek independently, but guided tours are incredibly inexpensive ($400 including entrance to Machu Picchu) and very enjoyable.

Where to stay: Camping along the trail!

Manu National Park

Volunteering in Manu National Park

Manu National Park

Incredibly lush, strikingly beautiful, and with more biodiversity than just about any other place on the planet, Manu National Park is one of the most spectacular areas to experience the Amazon Rainforest AND a phenomenal way to end your time in Peru. As the meeting place between the Tropical Andes and the Amazon Basin, this area is simply overflowing with unique flora and fauna, but it’s still amazingly remote and un-commercial compared to other spots like Puerto Maldonado or Iquitos. It takes more effort to get here, sure, but exploring a part of the Amazon that remains almost entirely untouched is a great reward for the long bus journey.

The best way to enjoy this magical part of the rainforest is to stay at an Ecological Reserve, like Chontachaka. Here, you’ll spend your days hiking to hidden waterfalls, searching for animals in the thick vegetation, and volunteering on conservation projects, like re-planting or invasive species removal, alongside passionate naturalist staff. It’s an incredibly raw and unpretentious experience, completely devoid of luxuries or even other tourists, but, as long as you don’t mind a little dirt under your fingernails and the occasional monkey in your bed, it is simply the best way to see the real Amazon.

Recommended time: 3-7 days

Highlights: Hike to hidden waterfalls and swimming holes in the Amazon; volunteer on ecological and conservation projects; nap in hammocks with monkeys; escape the city and reconnect with nature in the most peaceful of locations.

Getting there & away: If you’re staying at Chontachaka (see below), transport to and from Cusco is included, approximately 10hrs by bus each way.

Where to stay: Chontachaka Ecological Reserve offers open-air rooms and full board in the middle of the Amazon. With a resident monkey, heaps of hammocks, and total isolation (there were only 2 other people there during my whole week-long stay), this is the ultimate rainforest experience.

San Pedro Markets in Cusco

Incas & the Amazon: 2-3 week Peru travel itinerary from Lima to Manu National Park