Andrew Sears was off work for more than a year after being hospitalised with a compression fracture to his spine, a court heard.
But the father-of-one was unable to continue in his old role and, after another period of sick leave, was dismissed by Warburtons.
Wolverhampton Crown Court heard how on November 11, 2013 Mr Sears was cleaning one of the mixing machines at their Wednesbury bakery, a routine job he carried out every few weeks, when he lost his footing and fell nearly 2m.
Mr Sears, who had worked at the factory since 2007, was not able to return to work until December 2014. He was dismissed almost exactly a year later following another long period of sick leave.
The Health and Safety Executive (HSE) prosecuted Warburtons Ltd as a result of the incident.
The watchdog declared that there was a lack of training and supervision for employees working at height.
A spokeswoman said: "The Health and Safety Investigation found that Warburtons Limited routinely expected their workers to climb on top of the mixers to clean them.
"The workers were often unbalanced and would brace themselves to stop from falling.
"The workers were not adequately supervised and there had been no training on how the mixer needed to be cleaned at height."
Warburtons Limited, of Hereford Street, Bolton, pleaded guilty to breaching Regulation 6(3) of the Work at Height Regulation 2005 and was fined £2 million and ordered to pay costs of £19,609.28.
HSE inspector Mahesh Mahey added: "This should have been prevented, falls from height is one of the biggest killer in the workplace and even falls from fairly low levels can be extremely dangerous.
"Mr Sears' life has been changed forever but he his injuries could have been more severe."
Warburtons was originally founded by Thomas Warburton in Bolton in 1870. Today they are the largest baker in the UK. The firm opened its Wednesbury plant at Moorcroft Park in 2001.
It originally created 200 jobs but has since gone on to employ more than double that figure with the 185,000 sq ft site producing millions of loaves a week.
A Warburtons spokesman said: "We take the health and safety of all our people very seriously and are deeply saddened that on this occasion our procedures failed to protect Andrew.
"We have taken the necessary steps to prevent this happening again and will continue to review all health and safety procedures across our business.
"We have a very strong health and safety record across all of our manufacturing and distribution sites and we invest heavily in ensuring an accident free workplace for our employees, often working together with the HSE."