A good financial report is known for relevance, understandability, verifiability, neutrality, timeliness, comparability and completeness. This paper examines the significance of accounting system on performance of nonprofit organizations in Nigeria. The primary source of data was questionnaire for data gathering. Results were presented using percentages, averages and standard deviation. The target respondents were finance professionals of reputable nonprofit organizations in Lagos State, Nigeria. A total of 55 questionnaires were administered to the respondents, and 50 were retrieved representing 90%. These were analyzed using the One-Way ANOVA technique. Findings from the research depicts accounting system has significant influence on the performance of nonprofit organizations. It was recommended NPOs must maintain proper record keeping in line with international financial reporting standard; proper recruitment procedure must be adhered to, periodic training of accounting personnel on modern day software, annual audit of their financial statements, and the establishment of good accounting and internal control systems to curtail fraud.