The growing use of teleosts in comparative cognition and in neurobiological research has prompted many researchers to develop automated conditioning devices for fish. These techniques can make research less expensive and fully comparable with research on warm-blooded species, in which automated devices have been used for more than a century. Tested with a recently developed automated device, guppies (Poecilia reticulata) easily performed 80 reinforced trials per session, exceeding 80% accuracy in color or shape discrimination tasks after only 3–4 training session, though they exhibit unexpectedly poor performance in numerical discrimination tasks. As several pieces of evidence indicate, guppies possess excellent numerical abilities. In the first part of this study, we benchmarked the automated training device with a standard manual training procedure by administering the same set of tasks, which consisted of numerical discriminations of increasing difficulty. All manually-trained guppies quickly learned the easiest discriminations and a substantial percentage learned the more difficult ones, such as 4 vs. 5 items. No fish trained with the automated conditioning device reached the learning criterion for even the easiest discriminations. In the second part of the study, we introduced a series of modifications to the conditioning chamber and to the procedure in an attempt to improve its efficiency. Increasing the decision time, inter-trial interval, or visibility of the stimuli did not produce an appreciable improvement. Reducing the cognitive load of the task by training subjects first to use the device with shape and color discriminations, significantly improved their numerical performance. Allowing the subjects to reside in the test chamber, which likely reduced the amount of attentional resources subtracted to task execution, also led to an improvement, although in no case did subjects match the performance of fish trained with the standard procedure. Our results highlight limitations in the capacity of small laboratory teleosts to cope with operant conditioning automation that was not observed in laboratory mammals and birds and that currently prevent an easy and straightforward comparison with other vertebrates.