The money will be split between Macmillan Cancer Support, Child Poverty Action Group, One Parent Families Scotland and Poverty Alliance over the next two years.
The funding was announced ahead of the publication of the Scottish Government's child poverty strategy, which aims to tackle the causes of deprivation at an early stage.
Deputy First Minister Nicola Sturgeon said: "It is shocking that there are children in Scotland still living in poverty. We want to be a modern, dynamic country - and that is simply not possible while some in our society are trapped in poverty.
"We know there have been improvements to the number of people who are living in poverty in recent years - we also know that this progress is under threat from the changes to the welfare system. Today we are setting out how we plan to use £2.5 million to help fund advice and support services that provide front-line help to hard-pressed families."