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Background: A major challenge for primary care is to set priorities and balance demands with available resources. The registered nurses in this study are practice nurses working in primary care offices, playing a large role in initial assessments. The overall objective of this research is to investigate practices of communication and decision-making during nurses’ initial assessment of patients’ health problems in primary care, examine working mechanisms in good practices and develop feasible solutions. Methods: Project PINPOINT aims for a prospective multicenter study using various methods for data collection and analysis. A purposive sample of 150 patient‒nurse consultations, including 30 nurses and 150 patients, will be recruited at primary care centers in three different geographic areas of southwest Sweden. The study will report on outcomes of communication practices in relation to patient-reported expectations and experiences, communication processes and patient involvement, assessment and decision-making, related priorities and value conflicts with data from patient questionnaires, audio-recorded real-time communication, and reflective interviews with nurses. Discussion: This research will contribute to the knowledge needed for the guidance of first-line decision-making processes to best meet patient and public health needs. This knowledge is necessary for the development of assessments and decisions to be better aligned to patients and to set priorities. Insights from this research can empower patients and service providers and help understand and enhance feasible person-centered communication strategies tailored to patients’ level of health literacy. More specifically, this research will contribute to knowledge that can strengthen nurses’ communication, assessments, and clinical decision-making in primary care. In the long term, this will contribute to how the competencies of practice nurses and other professionals are organized and carried out to make the best use of the resources within primary care. Trial registration: ClinicalTrials.gov Identifier: NCT06067672.