A system and method for obtaining a clean fluid sample for analysis in a downhole tool are provided. In one example, the method includes directing fluid from a main flowline of the downhole tool to a secondary flowline of the downhole tool. While the fluid is being directed into the secondary flowline, sensor responses corresponding to the fluid in the secondary flowline are monitored to determine when the sensor responses stabilize. The secondary flowline is isolated from the main flowline after the sensor responses have stabilized. A quality control procedure is performed on the fluid in the secondary flowline to determine whether the captured fluid is the same as the fluid in the main flowline. Additional fluid from the main flowline is allowed into the secondary flowline if the captured fluid is not the same.