This research was aimed at evaluating the effect of Integrated Personnel and Payroll Information System (IPPIS) on Cooperative Societies in The Federal University of Technology, Akure (FUTA) Nigeria. Questionnaires were distributed to 50 Staff of FUTA, cutting across five different cooperative societies in the University during the month of May 2016. Their responses were analyzed using index rating and Chi-square method. The overall opinion of the respondents is that corrections of errors in salary and loan deductions are easily resolved within the University. It was observed that the University is taken advantage of a plug-in the IPPIS software known as GIFMIS (Government Integrated Financial and Management Information System) which enabled the University salary office to prepare pay schedule for each staff on monthly basis and upload same on the Federal Ministry of Finance IPPIS website. This plug-in has helped in domesticating the IPPIS in the Federal University of Technology, Akure such that the University staffs do not need to get to the office of the Federal Ministry of Finance in Abuja to correct any mistake in their salary. The positive experience of Federal University of Technology, Akure can be recommended to other Federal ministries, parastatals and units where the centralized IPPIS scheme is posing a challenge to smooth disbursement of staff’s salaries and allowances and loan repayment deductions in case of those who are member of cooperative society.