Extant literature has provided information about the conflict in Nigerian universities; however, there is a dearth of studies that specifically look into the causes and effects of conflict between academic staff and non-teaching staff. Against this backdrop, this study uses explanatory sequential mixed method design lenses to appraise the causes and effects of conflict between the two groups. Based on a population of 5487, comprising academic and non-teaching staff members of two selected universities in Nigeria, this study adopts a multistage sampling technique. In the first stage, Obafemi Awolowo University, Ile-Ife, and Olabisi Onabanjo University, Ago-Iwoye, were purposively selected from the strata of federal and state universities. The two universities have been experiencing conflict since their establishment. In the second stage, the Taro Yamane formula was used to obtain responses from 372 respondents. A proportion-to-size technique was utilised to prepare and administer questionnaires to respondents. Key informant interviews were also organised for 24 purposively selected interviewees. The interviewees included two executive members of the Academic Staff Union of Universities, two executive members of the Non-Academic Staff Union of Universities, four academic staff and four non-academic staff from each of the two universities. The quantitative data collected were analysed, using descriptive statistics, while the qualitative data gathered were subjected to a content analysis. The study revealed that factors like communication gap, poor human relations and differences in perception of duties are capable of causing conflict between the two groups. This conflict has adverse effects on the environments of the two universities.