Alongside his vocation he engaged in ethnography, archaeology, ecclesiastical history and botany, the latter being his greatest love. He was the first specialist in the former Hungarian state in complex Rubus (blackberry) genuses. He was the first to set down the taxonomy of various plants, while others - such as the bee orchid, Ophrys holosericea subsp. holubiana - were named in his honour. He was the author of more than 550 scholarly and popular works written in Slovak, Czech, German and Hungarian. A founding member of "Matica slovenská", he was also a member of a number of scholarly bodies both at home and abroad. For his life's work he was awarded an honorary doctorate by the Charles University in Prague in 1922.

Despite the substantial recognition he received, he remained true to the Slovak people from whose ranks he came, and believed in its culture and tradition.