The total of £12,818,835 in 2011/12 is £969,436 higher than the £11,849,399 claimed by Holyrood's politicians in 2010/11.
The rise is due to so-called winding-up expenses claimed by MSPs who either stood down or were not returned to the Scottish Parliament at the 2011 elections, Holyrood said.
Excluding these costs, the total expenses paid out to MSPs was just over £11.3 million, representing a decrease of just more than £500,000 on the previous year.
A total of 48 MSPs claimed winding-up expenses in 2011, which include staff salary costs, staff redundancy and office and accommodation costs.
A spokesman for the Parliament said: "Once election-related winding-up costs are set aside, we see a fall of more than £0.5 million in members' expenses, which reflects the two-year pay and expenses freeze that Holyrood has in place.
"The Parliament is on course to achieve a 12% saving over four years by 2014/15, which means its annual expenditure will be down by £9.5 million in real terms."
Party leaders' allowance claims fell from £39,829 to £38,368 in 2011/12, a difference of £1,461.
Stationary and postage provision fell by £15,129 from £471,296 to £456,167.
The salary, pension and national insurance contributions of MSPs' employees in 2011/12 was £9,659,381, including winding-up costs for staff of £1,485,026.
Expenditure on childcare vouchers totalled £34,308 while security-related and disability provision expenditure was £16,667.
First Minister Alex Salmond claimed £13,361 on expenses such as office rent, travel costs including mileage, and phone bills.
Labour leader Johann Lamont spent £17,831, which included overnight hotel stays in Edinburgh as well as taxi and train fares. The Glasgow MSP spent £800 on website costs and more than £1,050 on surgery advertising.
Conservative leader Ruth Davidson recorded £20,440 of expenses for 2011/12. Her expenses include £148 in June 2011, shortly after the Scottish elections, for MSP staff training entitled "dealing with difficult people".
Willie Rennie, leader of the Liberal Democrats, claimed £19,738, including almost £361 on return flights from Edinburgh to Heathrow in July 2011.
Meanwhile, Green Party co-leader Patrick Harvie spent £24,266 on expenses including rail passes, overnight hotel stays and other costs.
Labour MSP Anne McTaggart spent the most on books, totalling £141 on titles such as Public Speaking and Presentation for Dummies, and several works on Labour politician Barbara Castle.
MSPs spent a total of £6,608.32 on hotel meals, with independent MSP Bill Walker accounting for £609 and SNP MSP James Dornan spending £538 on meals.
Elsewhere, Margaret Burgess, minister for housing and welfare, spent just over £85 on a coat stand for her office while Environment Secretary Richard Lochhead claimed £368 for a computer desk.
Mr Walker went to budget retailer Poundstretcher to furnish his office, spending £5.99 on a table for the kettle in his constituency office.
MSPs spent a total of £12,706 on furniture and internal office decoration.
Between them, SNP MSPs spent just over £3,207 on training courses for staff on how to write effective press releases.