A port manager is configured to implement adaptive port ceiling assignment for background Input/Output (I/O) operations between heterogeneous storage arrays. The port manager generates a set of test I/O operations, applies the I/O operations to a port under test, determines a response time to complete the I/O operations on the port under test, and compares the response time of the current test with response times of a set of previous tests. Based on the test values, the port manager identifies a throughput inflection point for the port under test, which is used to set a maximum throughput of the port under test. The adaptive ceiling for the port under test is then set based on the maximum throughput times a ceiling percentage threshold value. The determined adaptive ceiling value is then used to prospectively limit background I/O operations on the port under test.