Mary was a woman who stood up for what she believed in, and this conviction brought her into conflict with religious leaders. She took a vow of poverty, which meant she had to beg for money. Catholic leaders didn’t like begging, but Mary refused to change her ways. The tension escalated into conflict over educational matters and Bishop Shiel felt that ‘she had incited the sisters to disobedience and defiance’ in the school she ran. He also, among other things, complained that they sang too much and as a result Mary was excommunicated by Bishop Shiel for insubordination in 1871.

Mary then took her plight to Rome to explain her predicament to the Pope. As a result the Josephites were reinstated in their habits during a ceremony which took place in St Ignatius Church, Norwood South Australia on Tuesday 19th March 1872, six months after the excommunication.   It seemed fitting that this date was chosen as it was the feast of St Joseph 1866 when the Sisters of St Joseph officially began at Penola.  However, despite her ordeal Mary never publicly blamed the Church leaders for their action.

"God gives me strangth for what is necessary"
                                     Mary MacKillop, 1907