Northampton Crown Court yesterday heard how around £80 had gone missing from the till in a week when the suspect was not working at the store.
On Monday (February, 13) the prosecution opened the case against Stuart Jenkins, 41, who is accused of murdering pensioner Arthur Brumhill in 1993 during a robbery, in which money was also taken from the till.
Jenkins had worked at the store on a Government placement scheme about 10 weeks before the brutal killing.
Mr Brumhill's body was discovered against a wall at the bottom of a stairwell at Paul Denton Pet and Garden Supplies in Wellingborough Road on January 21 that year. He had been left in charge of the store that week as the owners were on holiday.
But William Harbage QC, for Jenkins, said money had gone missing from the till throughout that week, not just on the night of the murder.
Cross-examining store owner Norma Denton, he said: "Every day you were away there was a shortfall.
"There was no sufficient note to explain the shortages."
He added that during the first week of January back in 1993 there was also a discrepancy in the region of £30, which was brought to their attention by Mr Brumhill.
Jenkins, now 41, of Ossett in Wakefield, did some work experience at the store for six weeks, back in 1992 as a 17-year-old.
His last day of work was November, 6, 1992.
He was charged with the offence in May 2015, having first been arrested shortly after Mr Brumhill's death. He denies murder.
Norma Denton told Northampton Crown Court that 76-year-old Arthur Brumhill 'wasn't allowed home until about 10-10.30pm at night'.
Giving evidence, she said the victim would often walk around a local park, which prompted the owners to give him a key to the shop.
Mrs Denton said: "Arthur wasn't allowed at home until about 10-10.30pm, so he would spend a lot of time at the shop.
"He used to go home for a short period mid evening from what I can understand and then he would return to the shop.
"Knowing Arthur, he was a lovely man. Dare I say we inherited him as much as the shop. We grew fond of him.
"We got him an easy chair, a comfy chair that he used to use upstairs. My recollection is that is was in the front room."
Mr Brumhill would often listen to his radio and read while sat upstairs in the kitchen and William Harbage QC said he would treat the shop "like home."
In February 1993 Mr Denton gave a police statement in which he described noticing how the pet store was left in an unusual state when he returned from holiday.
The court heard how he noticed the till tray was on the floor, which should have been kept in the toilet and locked with a side bolt from the outside.
He said this was unusual because "Arthur was very good at tidying up at the end of the day.
"Everything was in the right place."
Mr Denton also mentioned that a toolbox, which he expected to be kept under the bottom shelf, was pulled out onto the shop floor and pot plants in the kitchen were found laying 'on their side'.
A tyre lever, believed to be the murder weapon was "missing."
The trial continues.