Jamie Franklin, 32, is charged with shooting Tommy Foster and Stephen Line on 25 October, 2001.
A jury at Northampton Crown Court was told on Tuesday that the victims' bodies were burned and put into scrap cars before one was put through a car crusher.
Prosecuting, William Coker QC, said: "Tommy Foster has disappeared without trace.
"Stephen Line's charred and fragmented remains were eventually found in the boot of a burnt-out scrap car at Franklin's business premises.
"In the back of his head was a single bullet hole."
The prosecution said Mr Franklin killed the men to dodge more than £10,000 worth of debts.
Mr Franklin of Northamptonshire denies two counts of murder and Darren Anderson, 32, also of Northamptonshire, denies one count of perverting the course of justice.
The trial continues.
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