Labuan Bajo often pops up on every traveler’s bucket list, both local and international. You might be one of those who’s been dreaming of exploring the western tip of Flores Island. The stunning scenery, rich marine life, and the unique Komodo National Park make this place extra special. No wonder it’s a UNESCO World Heritage Site—after all, Komodo National Park is the only natural habitat of the mighty Komodo dragons.
If you’re currently busy Googling the best 3 days 2 nights itinerary in Labuan Bajo, you’re on the right page. This duration is just right to explore all the gorgeous islands around, and there are plenty of fun spots you won’t want to miss.
So, if you’re looking for a go-to guide on how to spend 3 days in Labuan Bajo, get ready to jot things down. Let’s break down the itinerary so you’ll have a clear idea of where to go once you’re there.
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A Quick Look at Komodo National Park
Before diving into the daily itinerary, let’s get to know Komodo National Park. The area is made up of three main islands: Rinca, Komodo, and Padar, plus a bunch of other smaller islands scattered around. You’ll find dozens of snorkeling spots here, so it’s no surprise that 3 days 2 nights might feel too short once you start exploring.
This is the natural habitat of the famous Komodo dragons, giant reptiles that can live over 30 years. The surrounding coral reefs are still healthy and diverse, making them a perfect home for fish, manta rays, and other marine life. With its stunning environment, Labuan Bajo isn’t just great for nature-lovers, but also for anyone wanting a laid-back escape in the far eastern part of Indonesia.
3 Days and 2 Nights Itinerary in Labuan Bajo
A trip to Labuan Bajo wouldn’t feel complete without exploring Komodo National Park—one of those UNESCO Heritage Sites that truly lets you go “back to nature.” Besides spotting Komodo dragons, you’ll be amazed by the landscapes that’ll leave you speechless. Another key thing you need to know is that you can only reach Komodo National Park and its surrounding islands by boat. That’s why 3 days 2 nights is a perfect timeframe to hop from island to island at a relaxed pace. Dive trips are also a popular activity during this itinerary, offering unique diving experiences near Komodo National Park. Below is an itinerary suggestion, where you’ll be sailing on a Phinisi boat to explore Komodo National Park.
Day 1: Sebayur Island – Taka Makassar – Manta Point
Taka Makassar, Komodo National Park | IndonesiaJuara Trip
- Depart from Labuan Bajo Port
Your adventure starts early in the morning. Usually, you’ll be picked up from your hotel or the airport and taken to Labuan Bajo Port. There, a Phinisi boat awaits. The moment you step on board, you’ll feel that premium holiday vibe. The cabins are comfy, and the outer deck is perfect for chilling while the sea breeze gently hits your face. - Sebayur Island
The first stop is Pulau Sebayur, known for its marine life. If you’re into snorkeling or even if it’s your first time, this is a great spot—colorful corals, plenty of fish, and usually clear visibility. Just gear up with a life jacket, snorkeling equipment, and follow your guide’s instructions. - Taka Makassar
After you’ve had your fill of underwater fun at Pulau Sebayur, the boat will head to Taka Makassar. It’s not really an island, more like a sandbar that appears when the tide is low. You’ll get that surreal feeling of standing right in the middle of the ocean, surrounded by nothing but crystal-clear water and soft white sand. Many travelers love snapping photos here because the scenery is so unique and photogenic. - Manta Point
Next up is Manta Point, a favorite among snorkeling enthusiasts. From the name alone, you can guess this is a spot where manta rays often show up. If luck is on your side, you might see a whole group of these graceful creatures swimming around.
After you’re done exploring, you’ll head back to the Phinisi boat and spend the rest of your day watching the famous Labuan Bajo sunset from the deck. This is the kind of sunset that’ll have you reaching for your camera (or phone) over and over again.
Day 2: Padar Island – Komodo Island – Pink Beach – Kalong Island
- Padar Island
Early in the morning, the boat will anchor near Padar Island. Time to rise and shine earlier than usual, because the sunrise view from Padar’s peak is worth every yawn. Be aware that the trek to the top is a bit challenging, though. The trail and steps are decently laid out, but the incline can be steep. Make sure you’re in good shape, take enough water, and wear comfy shoes. Once you reach the summit, you’ll be greeted by a jaw-dropping panorama—three or four crescent-shaped beaches with waters in different shades of blue. Many consider it one of the most stunning sunrise spots not just in Indonesia, but in the world. - Komodo Island
The next stop is the island that’s home to the world’s largest living lizard, the Komodo dragon. You have to stay close to your ranger or naturalist guide, because Komodos are wild animals that need careful handling. Don’t wander off on your own, and avoid snapping photos too close without proper guidance. Aside from spotting Komodos, the landscape here is also impressive. If you’re lucky, you might see a dragon waddling across your trekking path. It’s thrilling, but also a bit nerve-wracking! - Pink Beach
Afterward, head to Pink Beach, which has been all over Instagram these days. The pinkish hue comes from fragments of red coral mixing with white sand, resulting in a soft pink shade that’s super pretty. The waters around the beach are clear, so you can snorkel here too if you still have the energy. If you’re feeling lazy, just stretch out on the sand and snap some photos. Remember to pack sunscreen and a hat—because that sunshine can be fierce. - Kalong Island
By late afternoon, the boat will sail to Pulau Kalong. Here, the main attraction is watching thousands of bats fly out at dusk, creating a dramatic scene against the sky. The blend of orange-yellow twilight, bat silhouettes, and the gentle sea breeze gives the evening a magical feel.
At night, you’ll stay on the Phinisi boat again. No worries about comfort—most Phinisi boats have cozy cabins with proper beds, AC, and decent bathrooms. Drifting off to the sound of the waves and waking up to a sunrise on the open sea is definitely a highlight of the trip.
Read more: The Best Boat Options in Labuan Bajo
Day 3: Kelor Island – Manjarite Island
Manjarite Island | IndonesiaJuara Trip
- Kelor Island
On your last day, the journey continues to Pulau Kelor. Kelor Island is renowned for its stunning landscapes and outdoor activities such as hiking and snorkeling. It’s a great place for a short trek up a hill that overlooks beautiful ocean scenery. The trail is somewhat steep but much shorter than the one on Padar Island. From the top, you’ll see rolling hills and a turquoise sea dotted with passing boats. For those planning diving activities, consulting a nearby dive shop can be very convenient. - Manjarite Island
The final stop is Pulau Manjarite. This spot may not be as famous as Padar or Komodo, but it boasts underwater beauty that’s just as enchanting. The snorkeling area here is generally calm, with clear waters and well-preserved coral reefs. Fish of all colors swim around, making it perfect for beginners or anyone who wants a quick, relaxing dip.
After you’re done exploring, you’ll head back to Labuan Bajo Port and be dropped off at the airport or your hotel. By now, you’ll probably wish you had a bit more time—3 days 2 nights in Labuan Bajo really does fly by!
The Best Way to Explore Labuan Bajo
From the itinerary above, you can imagine just how epic it is to see Labuan Bajo, especially Komodo National Park. However, here’s a key point: most destinations in Komodo National Park are only accessible by boat. There’s no direct road or anything like that. So, your options are basically renting a private boat or joining an open trip.
If you’re picturing yourself coordinating a Phinisi boat rental, arranging food, snorkeling gear, and hiring qualified guides, that can be quite a hassle. On top of that, you’d need to talk routes and schedules with the boat captain. It’s easy to get overwhelmed before your trip even begins.
That’s why booking a tour with a trusted operator like IndonesiaJuara Trip can save you a lot of time, money, and stress. Whether you go for a private trip or an open trip, they’ve got everything covered—from the Phinisi boat, pro crew, and knowledgeable guides to meals and documentation. Their Labuan Bajo tour package already includes:
- Airport/Hotel pick-up and drop-off (Labuan Bajo area)
- A well-equipped Phinisi boat
- Meals and drinks throughout the trip
- Snorkeling gear
- Experienced tour guide and naturalist guide
- Documentation
Basically, you just need to bring yourself (and your budget), then show up ready to have fun. How simple is that?
Read more: Solo Trip Labuan Bajo: A Must-Visit Paradise in Indonesia!
Let’s Explore Labuan Bajo with IndonesiaJuara Trip!
So, are you already picturing yourself enjoying this 3-day, 2-night itinerary in Labuan Bajo Flores? From snorkeling at Pulau Sebayur, taking photos on Taka Makassar, spotting mantas at Manta Point, trekking up Padar Island, to coming face-to-face with Komodo dragons on Komodo Island—it’s a packed adventure that’ll run smoothly if you plan it properly.
But why organize everything by yourself if there’s a foolproof package from a reputable travel operator? IndonesiaJuara Trip has got you covered with transport, meals, and all the permits to enter the national park.
So, what are you waiting for? Book your Labuan Bajo Tour with IndonesiaJuara Trip and get ready to sail away on a Phinisi boat, snorkel with colorful fish, meet the legendary Komodo dragons, and watch mesmerizing sunsets in the middle of the sea!
Your 3-day, 2-night adventure in Labuan Bajo Flores will be over before you know it, but the memories will last a lifetime. Make sure to charge your camera, pack your bags, and set your wanderlust free. Safe travels!
