Disclosed are a system and a method for adaptive configuration of conflicting applications. An example method comprises collecting system configuration information from a computer system, including system hardware and software information. The method further comprises monitoring system resource utilization during execution on the computer system of a first program and one or more second programs. The method further comprises determining one or more critical levels of system resource utilization by applying fuzzy logic rules to the collected system configuration information. When the monitored system resource utilization exceeds the determined critical level for a predetermined period of time, determining, based on the collected software information, if the first program conflicts with execution of one or more second programs. Determining whether conflicting second programs are harmful to the computer system and changing configuration settings of the first program to resolve conflicts with the conflicting second programs that are harmless.