What to expect
After Arequipa and the Cusco region, the lowlands change the rhythm of the trip. Book a coherent Amazon stay, not just a flight: where will you sleep, how will you get there and when will you leave? Puerto Maldonado is the gateway. Four city nights are different from four nights at a forest lodge.
How it fits into a journey
Suggested plan: days 1–2 Lima (2 nights); day 3 fly to Arequipa, days 4–5 city (3 nights); day 6 fly to Cusco and day 7 city (2); days 8–9 Urubamba (2); days 10–11 Ollantaytambo (2); day 12 Aguas Calientes (1); day 13 Machu Picchu and return to Cusco, day 14 Cusco (2); day 15 fly to Puerto Maldonado, days 16–18 Amazon block (4 nights including any city night); day 19 return to Lima and day 20 Lima (2); day 21 departure. Total: 20 nights. Have the lodge confirm flight and transfer compatibility for days 15 and 19. If a Puerto Maldonado night is needed before flying back, use day 19 there and fly to Lima on day 20.