Barisal Divisional Special Judge's Court judge Dilip Kumar Bhaumik issued the sentence on Wednesday.
The officials are the former manager of the microfinance's Raipasha-Korhapur branch and officers Ratan Prova Halder and Ibrahim Khalil.
Prova Halder was present at the court when the verdict was issued. The two others are absconding.
The trio has also been fined Tk 500,000 each with a provision that they will have to be in jail six months more if they fail to pay the fine.
Court official Harun-Or-Rashid, referring to the case files, said the three withdrew Tk 85,000 as loans using accounts of nine customers between June 20 and July 7 in 2011 and embezzled the money.
The Anti-Corruption Commission prosecuted them at Kotwali Police Station on Nev 24, 2013 and submitted the charge-sheet on Feb 26, 2015.