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Integration is an important, albeit difficult, goal of science and mathematics education. This paper presents a framework and a research design proposal to identify preservice teachers’ (PSTs) integration performance of science and mathematics (IPoSM). It also presents the classification of PSTs’ level of integration in each phase of a problem-based learning (PBL) activity, within the proposed framework, and evidence of their work. The framework is organized in three levels of integration, based on current research, and detailed with specific integration indicators about an exemplary PBL activity, named STEM Bees. This PBL activity was structured as a research problem divided into two integrated problems. A qualitative methodology was used, focused on the application of the framework to the work of PSTs in that PBL activity. The final participants were 13 PSTs, organized in four working groups. In general, results show that PSTs’ integration performance was higher with the second problem than with the first problem. However, full integration with meaningful connections between science and mathematics ideas was achieved by almost all PST at the conclusion of the research problem. The IPoSM framework indicators proved to be useful for identifying the level of integration of science and mathematics in PSTs’ work in each phase of the PBL activity. Keeping the IPoSM framework in mind, teacher educators could elaborate more effective problem-based integrated approaches of science and mathematics in initial teacher education.