The critical situation in education caused by COVID-19 has significantly reduced the involvement of pupils from vulnerable groups, particularly those with low learning achievements. The aim of this study is to reveal the modeling of the sustainable educational process and the factors that ensure optimal learning achievements of pupils from vulnerable groups in general education schools in critical educational transformation situations. To reveal the factors ensuring the sustainability of educational processes, this study was conducted in three Baltic countries (Lithuania, Latvia, and Estonia) involving 1432 subject teachers from public education schools. The results of the study highlight that self-regulatory collaborative learning has a sustainable, strong impact on the achievements of pupils with emotional and learning difficulties in various (stable and unstable) educational environments in all three countries. The development of digital skills, digital scaffolding, and technological provision for pupils with special educational needs enabled their teachers to have a sustainable positive impact on pupils’ learning achievements in Lithuania.