Plant phenotyping and production management are emerging fields to facilitate Genetics, Environment, & Management (GEM) research and provide production guidance. Precision indoor farming systems (PIFS), vertical farms with artificial light (aka plant factories) in particular, have long been suitable production scenes due to the advantages of efficient land utilization and year-round cultivation. In this study, a mobile robotics platform (MRP) within a commercial plant factory has been developed to dynamically understand plant growth and provide data support for growth model construction and production management by periodical monitoring of individual strawberry plants and fruit. Yield monitoring, where yield = the total number of ripe strawberry fruit detected, is a critical task to provide information on plant phenotyping. The MRP consists of an autonomous mobile robot (AMR) and a multilayer perception robot (MPR), i.e., MRP = the MPR installed on top of the AMR. The AMR is capable of traveling along the aisles between plant growing rows. The MPR consists of a data acquisition module that can be raised to the height of any plant growing tier of each row by a lifting module. Adding AprilTag observations (captured by a monocular camera) into the inertial navigation system to form an ATI navigation system has enhanced the MRP navigation within the repetitive and narrow physical structure of a plant factory to capture and correlate the growth and position information of each individual strawberry plant. The MRP performed robustly at various traveling speeds with a positioning accuracy of 13.0 mm. The temporal–spatial yield monitoring within a whole plant factory can be achieved to guide farmers to harvest strawberries on schedule through the MRP’s periodical inspection. The yield monitoring performance was found to have an error rate of 6.26% when the plants were inspected at a constant MRP traveling speed of 0.2 m/s. The MRP’s functions are expected to be transferable and expandable to other crop production monitoring and cultural tasks.