Pupils at the schools have excellent relationships with teachers and the local community, an HMIE report also finds, but are not always encouraged as much as they could be to broaden their horizons.
The inspectorate's report considers how to "open up learning" in about 40 all-through schools in eight local authorities.
These schools are in an "ideal position" to track pupils' long-term progress, to organise activities involving different age groups, and are "well-placed to support young people's learning in the context of Curriculum for Excellence", it says.
But recent inspections find "only a few instances where schools are exploiting their all-through context to the full, and enabling young people to reap the benefits".
The report notes the "very high quality of relationships embodying mutual respect between teachers and learners". There are good relationships with families, although parents could be more actively involved in their children's education, and strong bonds between pupils.
"Young people in all-through schools tend to `look out for' each other, and younger children observe patterns of behaviour and examples of academic, personal and social achievements to which they can aspire," the report finds.
Local partnerships contribute to "wider social and cultural goals". The report cites attempts in Shetland to maintain the islands' dialect and musical traditions, and the schools' support for Gaelic in the Highlands and Western Isles.
Pupils do not always get enough help in deciding what to do after leaving school, and there is a "need for an increased focus on developing young people's awareness of the range of choices and routes of progression available to them throughout their broad general education".
The schools must also get better at self-evaluation, a main point for action identified in about two-thirds of inspection reports.
The 40 schools sometimes include nurseries, and some provide education to the end of S6. Most are small and in remote areas - one exception is Glasgow Gaelic School - and not all call themselves "all-through".