So-called "paunch contents", together with dung and straw, were allowed to overflow from a concrete midden that was supposed to keep them contained at Scotbeef Limited's plant at Bridge of Allan, Stirlingshire, which processes 2500 cattle and 15,000 lambs a week.
It entered a tributary of the Allan Water river.
Specialist environmental crime prosecutor Shona McJannett told Stirling Sheriff Court the incident, in January and February last year, was the result of "a clear management failure".
Heidi Archibald, defending, said the plant had taken steps to manage it by the time the incident was identified by SEPA, but had focused on clearing the midden rather than the area.
She said: "This wasn't a wilful ignoring of its obligations."
Sheriff Mark Thorley fined Scotbeef £26,250.