Systems and methods for automatically configuring network elements for in-band telemetry are disclosed. A controller of a configuration engine, which includes a flow analyzer and an INT configuration module, receives sampled packets and flow updates from network elements that are not yet configured for INT telemetry. The controller forwards the packets to the flow analyzer that extracts flow properties from the received packets, generates a flow summary along various metrics, and records it in a multi-dimensional matrix. A few metrics from top flows are selected and forwarded to the INT configuration module to identify network elements from whom packets containing the selected metrics were received. The identified network elements are automatically configured with the selected INT configuration such that INT telemetry data can be collected from them. Changes to the flow are dynamically accommodated by reconfiguring the network elements based on the telemetry data received after they have been configured.