Choosing which issues to discuss in the limited time available during primary care visits is an important task for complex patients with chronic conditions. We conducted sequential interviews with complex patients (n = 40) and their primary care physicians (n = 17) from 3 different health systems to investigate how patients and physicians prepare for visits, how visit agendas are determined, and how discussion priorities are established during time-limited visits. Visit flow and alignment were enhanced when both patients and physicians were effectively prepared before the visit, when the patient brought up highest-priority items first, the physician and patient worked together at the beginning of the visit to establish the visit agenda, and other team members contributed to agenda setting. A range of factors were identified that undermined the ability of patient and physicians to establish an efficient working agenda: the most prominent were time pressure and short visit lengths, but also included differing visit expectations, patient hesitancy to bring up embarrassing concerns, electronic medical record/documentation requirements, differences balancing current symptoms versus future medical risk, nonactionable items, differing philosophies about medications and lifestyle interventions, and difficulty by patients in prioritizing their top concerns. Primary care patients and their physicians adopt a range of different strategies to address the time constraints during visits. The primary factor that supported well-aligned visits was the ability for patients and physicians to proactively negotiate the visit agenda at the beginning of the visit. Efforts to optimize care within time-constrained systems should focus on helping patients more effectively prepare for visits. Physicians should ask for the patient’s agenda early, explain visit parameters, establish a reasonable number of concerns that can be discussed, and collaborate on a plan to deal with concerns that cannot be addressed during the visit.