Should I book a layover flight through an airline alliance?

It is rarely worth it. Because you must clear customs in Lima with your bags, you have to exit the secure area and re-enter, effectively making it a self-transfer anyway.

Are flights to Cusco often canceled?

Yes, specifically due to weather. Cusco sits in a mountain basin, and morning fog frequently delays flights. Always pick a flight arriving before 11:00 AM to give yourself a cushion.

How to Book Flights to Cusco

Fly into Lima (LIM) first, then book a separate domestic flight to Cusco (CUZ) on a local carrier like LATAM. Do not attempt to book a single international ticket all the way to Cusco, as you must clear customs and immigration in Lima regardless of your airline.

Book your international flight to Lima. Search for flights to Jorge Chávez International Airport (LIM). Aim to arrive in Lima at least 4 hours before your connecting flight to Cusco to account for customs, baggage claim, and re-checking bags.
Choose your domestic carrier. LATAM is the most reliable airline for the Lima-Cusco route, operating hourly flights. Budget options like Sky Airline or JetSmart are cheaper but are more prone to cancellations or delays; if you use them, ensure you have a long buffer time.
Book the domestic leg separately. Use the Peruvian version of the airline's website (select 'Peru' as your country/region) to get local pricing. Many international versions of these sites charge a significant premium.
Check baggage rules. Domestic fares in Peru often include only a small personal item. If you have checked luggage, ensure your domestic ticket specifically includes a checked bag, or pay the fee online in advance, which is 50% cheaper than at the airport.

Should I book a layover flight through an airline alliance?: It is rarely worth it. Because you must clear customs in Lima with your bags, you have to exit the secure area and re-enter, effectively making it a self-transfer anyway.
Are flights to Cusco often canceled?: Yes, specifically due to weather. Cusco sits in a mountain basin, and morning fog frequently delays flights. Always pick a flight arriving before 11:00 AM to give yourself a cushion.