The first sign that something serious was brewing was when, Con Lucey, the retired chief economist and one of its most respected officers, stepped down from its audit committee in August 2014 over concerns about the association's accounting procedures and transparency.
Throughout most of last year, cattle farmers' anger simmered away at the IFA's perceived inadequate response to the difficulties in the beef trade, particularly those surrounding young bulls.
This anger finally lead to grassroots-driven protests at the factory gates but they were quickly lifted by the association's leaders. Farmers were left feeling empty-handed and furious. Meanwhile, the recent high-profile response to the slump in dairy prices contrasted with a lack of decisive action on other commodities, including tillage and pigs.
It has also been suggested that at the heart of the issue was not money but rather Pat Smith's personality, which has been described as "abrasive".
There were also claims from some quarters that the IFA has become weak, stale and reactionary.
After Mr Smith resigned last week, IFA president Eddie Downey commended him for his role in the last round of the CAP Reform negotiations and securing tax breaks for farmers in recent budgets.
However, for farmers, the small things are also very important. For example, many felt that not enough had been done by the IFA in tackling the introduction of new driving licence requirements for towing trailers and the taxing of old tractors.
Last January, a number of counties supported a motion of no confidence in Pat Smith. President Eddie Downey countered with a motion of strong confidence and that storm passed.
However, it was the beginning of the end when Carlow county chairman Derek Deane read a letter to the executive council earlier this month that said the general secretary had been paid in excess of €400,000 in 2013.
Once this figure was out, the IFA had no option but to reveal the details.
I spoke to a number of farmers over the weekend. Their first response was shock, their second anger. Several spoke of cancelling their IFA membership and their levies.
They are hurting. They feel they have been kept in the dark and hoodwinked. They are angry that their hard-earned money, was used to fund such remuneration packages.
Nobody expects a good man to work for cheap, but many drystock farmers would scarcely earn in their entire working life what Pat Smith was paid in a year.
It may not affect its ability to deal with government, but what about the processors?
However, the biggest challenge will be to win back the trust of farmers. A strong united representative organisation is badly needed and time is a great healer. But if there was a call to arms any time soon, it might be hard to find people to take them up.
The ethos of the IFA has always been to support the leadership and defend the organisation at all costs but, whether the executive council realise this or not yet, this situation is actually bigger. This time, it's not enough to circle the wagons. Whatever is there, no matter how unpleasant, has to come out - now.
But how much blood-letting will be enough to satisfy the grass-roots? And, when that has been done, will it be too late to stop a potential haemorrhage of support?