Adam Readwin, 38, was found in possession of the images after police carried out a search at his then home in Stamford.
Lincoln Crown Court heard officers seized a mobile phone and computer equipment belonging to Readwin during the search.
Victoria Rose, prosecuting, said these devices were analysed by computer experts and found to contain both still and moving indecent images of children.
In total there were 1,215 Category A images, of which 28 were videos; 2,065 Category B images, of which 8 were videos; and 1,886 Category C still images.
A small number of images depicting bestiality and extreme and prohibited images were also found.
Miss Rose said the youngest age identified in the Category A images was around nine-years-old.
Readwin, now of Oldham Street, Manchester, pleaded guilty to six offences relating to possession of the indecent, extreme and prohibited images.
The court heard Readwin had no previous convictions and made admissions to both the police and probation service about his activity.
Chris Jeyes, mitigating, said Readwin could not access the vast majority of the incident images and only retained a small number of them.
Mr Jeyes added there was no suggestion at all of any contact offences by Readwin during his time with the Scouts.
“He would say his interest with Scouting was because he enjoyed it as a child and he continued to enjoy those activities, such as kayaking, as an adult.
“He was an assistant Cub Scout Leader, so was not on his own.”
Passing sentence Judge John Pini QC told Readwin he could only narrowly draw back from an immediate jail sentence because of his previous good character and his obvious remorse and candour.
“For a period just shy of a year you were looking at indecent images of children,” Judge Pini said.
But the judge accepted Readwin committed no offences during his role as a Scout and added: “I am satisfied you are susceptible to rehabilitation.”
Readwin was sentenced to 14 months imprisonment, suspended for two years, and must also complete 50 rehabilitation days.
He was also made the subject of a Sexual Harm Prevention Order which will last for five years.