Archaeological investigations prove that people lived in Bubiai already in the 5th century. The Bubiai hill-fort had long been famous as an important defence centre. The defensive castle in Bubiai was mentioned in the historical sources already in the 14th century. 

As a Manor Estate Bubiai started to form in the junction of the 18th-19th centuries when after the last partition of the Polish-Lithuanian Commonwealth, the Russian Empress Jekaterina II gave Bubiai as a present to the Russian noblemen – Counts Zubovai. It is rather difficult to define the date when the Manor Estate buildings remaining nowadays had been built. Supposedly, some parts of the Manor appeared in the 4th decade of the 19th century, while the others in the middle of the century and the rest at the end of the 19th century or in the beginning of the 20th century. 

Bubiai reached its peak of prosperity and growth while Dmitrijus Zubovas inherited the Manor Estate and started to manage it. The new host of the Manor Estate had finished the Agronomic Sciences in Hohenheim and began the intense farming here. He used all the theoretical knowledge in his farm where he was developing stockbreeding and dairying. As well he constructed new buildings and tried to modernise the farm work.    

Since the end of the 19th century the Bubiai Manor Estate had been not only an exemplary farm, but also an education centre. Immediately after moving into the Manor the Count Zubovas opened an Elementary School, where Lithuanian was taught. In 1910 a Lower Three Forms’ Livestock and Dairy School was established in the Manor Estate. Dmitrijus Zubovas used to teach and manage the school by himself. People from different areas of Lithuania and even from the neighbour countries used to come to study here.  

Since 1894 in Bubiai, just like in the other manors of the Zubovai, there were evening outings organised. It was one of the activity forms of the fostering Lithuanianness. Such outings were not only a place to have fun, but also there Lithuanian speeches were made, various discussions about the free and independent Lithuania were initiated and also the counsels related to the organising issues of the Lithuanianness took place.     

In 1934 in Bubiai there was commemorated the forty years’ anniversary of the outings held. About 5000 people participated in the Festive outing. Various amateur events, performances, alive pictures were organised just like it had been during the first outings. Moreover, fairs, games and dancing were organised, as well.

Dimitrijus Zubovas was also a guardian of the book-smugglers. There used to be a strategic road through Bubiai, leading from Saint Petersburg to Konigsberg. This road was rather popular among people who transported the Lithuanian press. The Tsar’s gendarmes guarded this road intensely, thus, the Count Zubovas had to shelter the book-smugglers or to look for the ways how to sweeten the gendarmes. 

Dmitrijus Zubovas ruled the Manor Estate together with his wife Tatjana Zubovienė. He met his wife in the Manor of Ginkūnai ruled by his brother. Tatjana Molas from Saint Petersburg was invited to Ginkūnai in order to teach Dmitrijus Zubovas’ nephew Vladimiras.

Dmitrijus and Tatjana Zubovai got married in 1895. They had an only son Nikolajus, who died during World War I from dysentery, and 5 daughters, one of whom, died being very young. As grown-ups Dmitrijus and Tatjana’s daughters did not move away from the culture of manors and a farm life. Tatjana Zubovaitė married the landlord Jurgis Ropas. Kotryna Zubovaitė married the governor of Klaipėda region. He was one of the “Pienocentras“ (Eng. Milk centre) founders - Vladas Kurkauskas. Darija Zubovaitė married an agronomist, the Minister of the Agriculture Stasys Putvinskis-Pūtvis. While Elena Zubovaitė married an agronomist, the head of “Aušra“ museum - Česlovas Liutikas.

After the death of Dmitrijus Zubovas until the nationalization of manors in 1940 the Bubiai Manor was ruled by Dmitrijus and Tatjana’s daughters.