Before coming to Navadvipa, Jagannatha dasa Babaji performed his bhajana at Surya-kunda in Vraja. In the latter part of his life he came to Navadvipa-dhama. At this time he was considered by the Vaishnavas, including Bhaktivinoda Thakura, to be the most advanced rasika Vaishnava in Vraja-mandala, Gaura-mandala and Jagannatha Puri. He was therefore known as Vaishnava- sarvabhauma, or the chief of the Vaishnavas. At the request of Srila Bhaktivinoda Thakura, in 1893, he confirmed the discovery of the birthplace of Sri Caitanya Mahaprabhu at Yoga-pitha in Sridhama Mayapur.
Some Stories from his life :
In his old age, Babaji Maharaja was nearly blind. Many people would come to see him and to offer him donations for the service of Sri Krsna. Bihari dasa would keep all these donations in a bag. One day, Babaji Maharaja said, “Bihari! How many rupees have I got?” Bihari dasa had put some rupees aside for some service he had planned to render Babaji Maharaja. When asked by Bihari placed some rupees in his hand and kept twelve Rupees aside. Despite his eyesight failing, Babaji Maharaja detected the discrepancy. “Bihari!” he said, “Why have you kept twelve Rupees aside? Give me all the rupees!” Smiling, Bihari surrendered the remaining coins to his guru. The total came to two hundred rupees. Babaji Maharaja ordered Birari dasa to take the money at once and buy rasagolas, to feed all the cows in Nabadwipa dhama.
Once Babaji Maharaja was on the banks of the Ganges, living under a make shift canvas tent. Nearby that place there lived a dog with five puppies. Whenever Babaji Maharaja would take prasada, the dogs would come around and lick the food from his plate. When Bihari dasa caught hold of one of the dogs to drive it off, Babaji Maharaja told him: 'Bihari! If you wish to drive these dogs off, you may take my plate away as well. I shall not eat today.' When Bihari complained, 'But guru maharaja – these dogs are unclean!' Babaji Maharaja remarked, 'No. These dogs are residents of the holy dhama. You may not abuse them.'
One day, Sri Babaji Maharaja remarked about the professional readers of Srimad-Bhagavatam, 'This kind of professional Bhagavata kirtana is simply prostitution. Those who make their living by reading Srimad-Bhagavatam are offenders to the holy name of Krsna. No one should listen to the kirtana and Bhagavatam readings that they produce. And one who listens to such offensive readings and thus commits offenses against the holy name of Krsna certainly go to hell. Those who are involved in this professional reading should immediately give it up. Such a person should worship the residents of Vrndavan with great care and attention, considering himself most fallen, and thus pray for forgiveness.'
When Srila Bhaktivinoda Thakur was looking for the actual place where Sri Caitanya Mahaprabhu's birthplace was, he asked Jagannatha dasa Babaji Maharaja to go with him. During the many changes in the course of flow of the mighty Ganges River, some parts of the sacred 'dhama' of Navadwipa (nine islands) had changed. The Ganges had revealed old and lost places and reclaimed new ones. To his surprise Bhaktivinoda Thakur discovered that the modern day city called Navadwipa was not more than 100 years old and therefore wasn't the Navadwipa of Sri Caitanya. Some said the birth site was on a place now in the Ganges, while some said it was in the city of Navadwipa.
Dissatisfied, Bhaktivinoda pushed on looking. He found some antiquarian maps and government records, and authentic books written at the time of Lord Caitanya, all of which agreed that Mayapur Navadwipa Dhama is situated on the east bank of the Ganges.
One day from the terrace in his house he saw a light coming from a place across the Ganges. He wondered what it was, and then crossed over to Antardwipa the next day.
Upon reaching the exact spot, to his amazement he found several large mounds covered with sacred Tulasi plants on land owned by Mohammedans. There were rumours locally of strange lights and sounds, so the owner, believing it to be haunted, would not go there. Many old babajis of the time, however, believed this to be the actual birthplace of Sri Caitanya Mahaprabhu. Convinced it was true, Bhaktivinoda, inspired by Jagannatha dasa Babaji, went there to the spot, with Jagannatha dasa Babaji being carried in his basket.
Due to his old age, Srila Jagannatha dasa Babaji couldn't open his eyes, but had to forcibly open them with his fingers, what to speak of walk. If he went anywhere he was carried in his basket by Bihari Lal, but upon arriving at the transcendental site, he leapt out of the basket and danced in ecstasy shouting, “Haribol!” and “Gauranga!” and “Ei to Nimai Janmabhoomi!!”(This is the Birthplace of Nimai!) definitely establishing it to be the very same birthplace of Lord Caitanya.