Barry Hermon, 68, and Dennis Morgan ran Able Skips in Newport.
Cardiff Crown Court heard the pair consistently breached the 1,000 tonne limit of waste they were allowed at their site, reaching 10,500 tonnes.
Morgan was told he had escaped time in prison in part due to the recent ill health of his fellow defendant.
Able Skips was first issued with a permit to store controlled waste in 2004 but it was not long before it was in the sights of Environment Agency Wales.
Between 2006 and 2008, despite warnings to clear waste, a prosecution and fines totalling almost ?30,000, the company consistently exceeded its waste limit allowance.
Dennis Morgan faces three years in jail if he does not pay the Proceeds of Crime order Waste that could no longer fit into the unit was left piling up outside.
At the height of the operation, the firm was taking an income of ?1,000 a day
The firm's two directors were each given suspended prison sentences of 10 months.
Judge Nicholas Cooke QC said they had been motivated by greed and that nobody should have sympathy for them being left penniless due to the prosecution.
He added that had this case been dealt with quicker, they would have faced a prison sentence.
In court it was said the pair had received ?965,000 overall.
Hermon had realisable assets of ?230,304 and Morgan's were worth ?261,269.96. Both men have been ordered to pay the money back or face three years in prison.
The Welsh Government has agreed to put ?142m into the project Public consultation has begun over multi million pound plans to process non-recyclable waste in north Wales.