You land on Mactan, not in Cebu City
Mactan-Cebu International Airport sits in Lapu-Lapu City on Mactan, a separate island off Cebu’s east coast. Cebu City is on the main island. That distinction matters before you book a hotel, because an arrival-night bed on Mactan avoids crossing the channel just to come back toward the airport the next morning.
If the trip starts with an early onward flight, sleep on Mactan. If the next move is a city bus, a ferry, or time in Cebu City, cross after landing and stay on the main island. Mandaue sits between the bridge approaches and Cebu City, so a map can make everything look close while traffic has other ideas.
Foreign arrivals also need eTravel before landing. Use the Philippine government’s eTravel site or the eGov PH app, save the QR code offline, and ignore third-party sites asking you to pay for registration. Do that before the travel day gets complicated.
If your trip is actually a Mactan resort stay, resist the reflex to book Cebu City because the airport search says Cebu. Mactan itself has a strip of beach resorts, and staying there keeps the bridge crossing out of the arrival entirely. Geography can save more hassle than another round of hotel comparison.
So decide where the next morning begins before choosing the arrival-night hotel.
The terminal change is landside, not a corridor behind security
MCIA splits international and domestic flying between separate terminals standing side by side. The international terminal has the curved timber roof you see in airport photos. The important detail is less photogenic: there is no airside connection between the buildings.
If you arrive internationally and continue on a domestic flight, you clear immigration, collect your bag, move landside to the domestic terminal by shuttle or on foot, and check in again. Reverse the direction and the same basic problem remains: changing buildings is not the same thing as walking between adjacent gates.
This matters more on separate tickets. On separate tickets, the second airline owes you nothing when the first one runs late. If your itinerary involves connecting through Hong Kong before arriving at CEB, look at the Cebu side of the booking too, not just the long-haul connection.
I would give a terminal change room to breathe. A cheap separate-ticket connection stops being clever when immigration, baggage, and another check-in all have to behave perfectly.
Crossing into Cebu City: pick the ride for the luggage you have
Road traffic leaves Mactan across the Marcelo Fernan Bridge, Mactan-Mandaue Bridge, or the Cebu-Cordova Link Expressway. Weekday rush periods jam the crossings, so the route that looks short on a phone can become the part of the arrival that eats the buffer.

MyBus picks up outside the airport terminals and carries luggage, with city routes serving SM City Cebu and Cebu IT Park via Ayala Center Cebu. It makes sense when a stop is useful to you. If your hotel still needs another ride from the bus stop, count that extra transfer before deciding the bus is the simple option.
Taxis come in yellow airport cars and white city cabs. Ask for the meter. Grab also works at the airport, which removes the need to explain a hotel address while standing beside luggage and pretending you heard the driver correctly over terminal traffic.
Rush-hour bridge traffic is the variable I would respect here. The older bridges land in Mandaue, while CCLEX runs from Cordova straight to the South Road Properties in Cebu City. Pick the crossing around the destination instead of assuming every bridge is interchangeable.
Book the ride that gets you to the actual door you need, not the transport option that looks tidy in isolation.
The beach may start with a ferry terminal or a bus terminal
Bohol changes the shape of the trip again. Fast passenger boats run from Cebu City to Tagbilaran, and OceanJet is the operator I would check when the travel day approaches. Bring identification that matches the ticket name. If Bohol is the real destination, also compare flying into Bohol-Panglao International Airport instead of automatically building an airport-to-city-to-pier chain through Cebu.

Moalboal is a road problem rather than a boat problem. Ceres buses leave Cebu South Bus Terminal for the west coast. The useful sign is “via Barili.” A bus marked “via Oslob” heads down the other side of the island, which is an impressively efficient way to be moving while getting farther from the plan.
Malapascua adds another transfer. Start from Cebu North Bus Terminal near SM City Cebu, travel toward Maya port, then continue by boat. The boat leg is exactly why I would not build the trip around a late arrival on Mactan. If the sea connection has stopped for the day, enthusiasm does not become a ferry.
Pick the beach before you buy the Cebu flight. The name “Cebu” covers several very different ground-and-water chains.
Weather decides whether the last link still works
Cebu stays warm through the year, but the travel chain changes with the season. The drier stretch runs roughly from December through May. The wetter months follow, and they bring typhoon risk and rougher seas.
The Philippine Coast Guard suspends sailings when the sea turns rough. That matters more than whatever neat sequence you built at home, because a flight can arrive normally while the boat you planned to catch is going nowhere.
I would avoid making a wet-season arrival depend on a same-day boat connection that has no room for disruption. Put slack between the plane and the sea, especially when the beach requires another road leg after the crossing.
Cebu rewards a simple booking habit: work backward from the bed. Find the island, town, or beach where you are actually sleeping, then trace the boat, bus, bridge, terminal, and airport in reverse. If the chain still looks cheap after that, buy it.