An independent MP accused of theft has been found guilty of 20 counts of theft, after a three-month trial.

Member for Mount Gambier Troy Stephen Bell, 51, had pleaded not guilty to 20 counts of theft and six counts of dishonest dealing with documents when the trial started in June.

He was found not guilty of just one count of dishonest dealing with documents.

On Thursday, the jury returned unanimous verdicts on all counts except for two theft charges — on which they instead reached a majority guilty verdict, where 10 or more jurors agreed.

The jury delivered its verdicts for each charge after deliberating for more than two days.

Prosecutors had told the jury Bell abused his position as a Department for Education employee to steal more than $430,000 from not-for-profit educational organisations between 2009 and 2013.

They had alleged he used the money, which was intended to support disengaged and vulnerable high school students to re-engage in study, to instead fund home renovations and pay credit card debts.

Lawyers for Bell, however, had told the jury the entire prosecution case against him was a "mad rabble" and had "more holes than a Balfours crumpet".

Opening the trial in June, prosecutor Jemma Litster told the court Bell abused his position of power at the helm of the Independent Learning Centre (ILC) in Mount Gambier, which he had helped establish in 2006.

She said it was alleged that the funds he stole — totalling $436,023.24 — were intended to be used for the purpose of not-for-profit associations in the South-East, which invoiced Millicent High School to fund the ILC.

Ms Litster had told the jury the offending had gone unnoticed because Bell was "well-liked" and "trusted in his profession and social circle".

"The view people held of him from the outside looking in, was one of the factors his fraud went on unnoticed for quite some time," she said.

During the trial, the jury was played an intercepted phone call between Bell and former Liberal leader Isobel Redmond, in which he asked for her help to find "a pretty good lawyer".

The court had heard the alleged offending ended in 2013 when Bell quit to pursue a career in politics.

He won the March 2014 election as a Liberal candidate, but quit the party after he was charged in 2017.

Since then, he has been re-elected as the independent member for Mount Gambier twice, in 2018 and 2022.

Bell's defence barrister, Nick Healy, had told the jury the ILC had "thrived" and grown under Bell's leadership.

He said it was an "entirely detached as a matter of commonsense" that Bell would steal from the program.

"He had a very strong relationship with the students, he knew how to connect with them in a non-judgemental way," he said.

"He was innovative, thought outside the square, came up with ideas that the kids loved and was entirely authentic, who had the kids educational opportunities at the forefront of his mind at all times."

Mr Healy told the jury the prosecution case against his client had been "all sizzle and no sausage" and an attempt to discredit Bell.

"The entire prosecution case is misguided, it is misleading, it is confused and confusing, and it is internally inconsistent," he had told the jury. 

Outside court, Bell did not comment and walked straight into a waiting car.

Mr Healy also declined to comment on behalf of his client.

Judge Rauf Soulio thanked the jury for their "crucial" service and the "clear attention" they paid though the three-month trial.

"It has been apparent during the course of this long trial that you have been very dedicated fulfilling your duty as jurors," he said.

Judge Soulio also excused them from any future jury duty.

Bell will return to court at a later date for sentencing.