A storage array that uses NVMEoF to interconnect compute nodes with NVME SSDs via a fabric and NVME offload engines implements flow control based on transaction latency. Transaction latency is the elapsed time between the send side completion message and receive side completion message for a single transaction. Counts of total transactions and over-latency-limit transactions are accumulated over a time interval. If the over limit rate exceeds a threshold, then the maximum allowed number of enqueued pending transactions is reduced. The maximum allowed number of enqueued pending transactions is periodically restored to a default value.