Integrated exercises that mimic daily tasks are generally preferred for improving performance and the later stages of rehabilitation, but it is unknown whether integrated core exercises are better than isolated core exercises at improving muscle activation for hypertrophy. The aim of the study was to compare the electromyographic (EMG) activity in rectus abdominis, oblique externus, and erector spinae while performing three conditions of integrated core exercises (lunges) with three isolated core exercises (prone bridge, side bridge and back extension). The three conditions of lunges were: on a stable surface, unstable surface and with external resistance to the trunk using an elastic band. The external resistance was measured with a force cell and peaked at 75N. After one familiarization session, all exercises were performed in one experimental session in randomized order. The isolated core exercises were performed in 20 seconds and the time performing the five repetitions with lunges was matched (20 seconds). Significantly greater peak normalized EMG activity were observed in the isolated core exercises compared to the three integrated core exercises (P<0.001) with two exceptions. For the oblique externus, the isolated core exercise was only greater than the stable lunge. Lunges with elastic bands only demonstrated greater peak erector spinae activation compared the other lunge conditions. Comparing the mean EMG activity between the isolated and three integrated exercises, greater muscle activations were observed performing the isolated exercises (P<0.001). Unstable lunges did not increase the peak or mean core muscle activations. In conclusion, mean and peak EMG activity performing the isolated exercises were in general greater than the three condition of lunges. Based on these results, we recommend using isolated core exercises when the primary goal is to improve muscle activation and elicit hypertrophy, but integrated exercises once adequate initial hypertrophy is achieved.