The authority launched its first eco-friendly school earlier this year when Cumbernauld and St Andrew's primaries opened their doors on a new joint campus - itself a contentious development.
Roof-mounted solar panels add to the renewable energy initiative being pioneered under the public private partnership (PPP) and other schools are poised to join the "green" building scheme.
David Alexander, convener of the Kirk's education committee, told church reps at the Edinburgh conference that environmental issues were central to the design of PPP schools.
Mr Alexander, a former depute director of education in Strathclyde, has acted as an adviser to PPP companies and to local authorities on rebuilding programmes. Under questioning, he accepted there were often conflicts between cost and design - but "if schools were like Asda Superstores, they would not make a statement".
It was not in the interest of the private sector to put up shabby school buildings - it had to bear the costs of maintenance and financial penalties over 30 years. "One Glasgow head said he had reported a broken window and it had been fixed right away when it used to take six months," he said.
Mr Alexander re-emphasised the General Assembly commitment to sharing joint campuses with Roman Catholic schools but admitted that some on the Church of Scotland side were uncomfortable about the situation, "especially in the west of Scotland".
Headteachers were absolutely crucial to the running of joint campuses, which share premises such as kitchens and sports facilities. Some shared staffrooms.
Mr Alexander advised church reps monitoring councils' PPP schemes to watch out for issues around disabled and community access and security.
Flexibility over classroom space was also important. Some teachers favoured open-plan for the early years but "cellular" approaches for older pupils.
The Scottish Executive's pledge to cut class sizes would have "horrendous" implications for buildings, he speculated. Mr Alexander said the biggest change in school building was the transfer of risk to the private sector.
If it got its sums wrong, it had to bear the cost. Some early schemes underestimated the extent of vandalism.
Ewan Aitken, Edinburgh's education spokesman, said the city had improved 15 per cent of its building stock in four years, affecting 18 buildings. Ten schools had closed.
Mr Aitken defended the PPP model as a long-term investment by politicians who were often accused of short-termism. Traditional building routes also involved work with private contractors who made a profit.
"You do not get a cheque from the Scottish Executive. You get permission to borrow money which you have to pay back," Mr Aitken stated.