Certain aspects relate to systems and techniques for endoscopically-assisted percutaneous medical procedures. A method can include inserting a first medical instrument having an elongated shaft and a first position sensor into a treatment region of a patient through a natural orifice of the patient. A first position of the first medical instrument within the treatment region can be determined with the first position sensor. A target location can be defined within the treatment region that is distanced from the determined first position. A second medical instrument can be percutaneously guided toward the target location. The method can be performed on a robotically-enabled medical system.