The spread returned to supermarket shelves towards the end of March 2013, roughly three months before the end of the church's last financial year.
After deductions were made for charitable activities and other expenses, including $8.9 million worth of "appropriations" to church entities, the religious organisation reported a net surplus of $5.2 million for the year, up from a net deficit of $56.3 million in the prior comparable period.
The church's businesses are exempt from paying company tax because they are registered with the New Zealand Charities Commission.
James Standish, communications director for the South Pacific Division of the Seventh-day Adventist Church, said most of the 3 per cent revenue growth reported in the latest accounts had come from other areas of the church's trading activities, rather than Sanitarium.
"Sanitarium's total revenue has remained steady over the last two years with any increases being largely offset by the Marmite shortfall during this period."
Standish said the "substantial cost" of the Marmite shortage had been covered by insurance.
The Seventh-day Adventist Church booked $7.2 million in insurance proceeds in the latest financial statements.
Sanitarium general manager Pierre van Heerden said Marmite sales had returned to pre-shortage levels since sales resumed 10 months ago.
"We're back to the penetration levels we had prior to the earthquakes," van Heerden said.
"It's taken a bit of time to get all of our different (product) sizes into the marketplace."
He said Sanitarium - which also produces Weet-Bix and Skippy Cornflakes - stood to gain a small amount of benefit from an improving economy.
The company was relatively recession-proof, van Heerden added.
Sanitarium has faced criticism in the past for the income tax exemption it receives.
Its profits help fund the church's charitable activities, which include the Adventist Development & Relief Agency, schools and aged care facilities.
In a 2001 submission to an Australian inquiry into the definition of charities, New York-listed cereal giant Kellogg's complained that Sanitarium's tax exemption gave its Australasian rival an unfair advantage.
Sanitarium says on its website that it operates exclusively for charitable purposes.
It says it does not hold a "preferential position" in the market as a result of its tax-exempt status.
The Inland Revenue Department considers the "advancement of religion" a charitable purpose that qualifies for a tax break.