Amazon first, then the Andes
Start in the rainforest. It is at sea level, so your body has nothing to adjust to, and the days are built around the river rather than early starts. When you fly to Cusco afterwards, we take you straight down to the Sacred Valley at about 9,000 ft (2,750 m), a gentler first night than the city, and reach Cusco itself last.
The reverse works, but it puts the altitude at the start and the long travel day late in the trip, when you would rather be slowing down.
How many days you need
Ten days and nine nights is the minimum that does both justice: one night in Lima, three on the river, two in the Sacred Valley, one beside Machu Picchu and two in Cusco. Twelve lets you add a seven-night sailing or a second Machu Picchu night. Eight is possible with a lodge instead of a cruise, but the Andes get tight. International travel days are extra.
Cruise or lodge for the Amazon half
A cruise with Aqua Expeditions from Iquitos gives the most wildlife and the most comfort, at the cost of a fixed sailing date and a Lima connection at each end. Inkaterra Reserva Amazónica near Puerto Maldonado is one short flight from Cusco and slots in more easily. Our guide to cruise vs. lodge goes into the choice; in short, choose the cruise when the Amazon is a reason for the trip, the lodge when it is a contrast to the Andes.
The flights in between
The cruise route means Lima to Iquitos at the start and Iquitos to Cusco, via Lima, on the day you disembark. The lodge route is Cusco to Puerto Maldonado and back. Flights are not included in our published prices, but we book them for a small fee and manage every connection, with a private transfer waiting on each side.
The journey we built for it
Amazon & Andes is our ten-day answer: three nights aboard Aqua Expeditions in the Pacaya-Samiria Reserve, then Inkaterra hotels in the Sacred Valley, Aguas Calientes and Cusco with private guides throughout. For the lodge version, Exploration of Peru pairs three nights at Inkaterra Reserva Amazónica with the same Andes route. Both start from a written proposal for your dates and are tailored from there.