The improvement programme due to start next week comes after visitors complained about a lack of rest rooms in the decade-old building.
The new toilets are due to be completed in July after the work went out to tender with the total cost put at £535,000. It includes a special facility to cater for people with severe disabilities and a doubling of the number of toilets in the main foyer.
The Parliament said the pressure on public toilet facilities had been observed "over a number of years" and the opportunity to upgrade the facilities and increase capacity was being taken in advance of this year's Festival of Politics and the return of the Great Tapestry exhibition this summer.
Lothian Labour MSP Kezia Dugdale said: "Half a million pounds is an awful lot of money to spend a penny.
"It's absolutely right and appropriate to spend money on adaptations to make sure no-one is excluded from visiting the Parliament, but this money goes way beyond that."