Officers from Strathclyde Police found more than 2500 plants on a disused industrial estate in Woodilee Road, Kirkintilloch, yesterday.
Police described the breakthrough after a tip-off as a "significant cannabis cultivation".
It came after police discovered a kilo of cocaine, worth £100,000, in unconnected raids on two properties in the East Dunbartonshire town on Wednesday.
In the latest raid, officers discovered an extensive heating and lighting system which was being used to encourage the growth of the plants.
One eyewitness said: "It is just an old building, you wouldn't look at it twice. You definitely wouldn't think it was being used as a drugs factory.
"I heard the police helicopter out earlier this morning, around 10am."
Chief Inspector Roddy Irvine of Strathclyde Police said: "This operation demonstrates our determination to rid our communities of drugs.
"This intelligence operation has led to a substantial recovery and illustrates once again that officers are working extremely hard to ensure drugs are kept off our streets and out of our communities.
"This operation is a result of a tip-off and is proof that through effective intelligence gathering, help and support from the local community we can successfully detect and arrest those involved in criminality. I have no doubt this recovery will cause serious disruption."
On Wednesday, officers searched two houses, one in Blackthorn Avenue and the other in John Street, Kirkintilloch.
Officers recovered approximately a kilo of what's believed to be cocaine in each of the properties.
Two men, aged 24 and 25, have been arrested in connection with the seizure and are due to appear at Glasgow Sheriff Court later today.
Police are not linking the two incidents.
Police renewed their appeals for the public to be vigilant and if anyone suspects suspicious activity they should contact the force.