Although there are many studies demonstrating increased trunk activation under unstable conditions, it is not known whether this increased activation would translate into meaningful trunk strength with a prolonged training program. Additionally, while balance-training programs have been shown to improve stability, their effect on specific joint proprioception is not clear. Thus the objective of this study was to examine training adaptations associated with a 10-week instability-training program. Participants were tested pre-and post-training for trunk extension and flexion strength and knee proprioception. Forty-three participants participated in either a 10-week (3 days per week) instability-training program using Swiss balls and body weight as resistance or a control group (n = 17). The trained group increased (p < 0.05) trunk extension peak torque/body weight (23.6%) and total work output (20.1%) from pre- to post-training while the control group decreased by 6.8% and 6.7% respectively. The exercise group increased their trunk flexion peak torque/body weight ratios by 18.1% while the control group decreased by 0.4%. Knee proprioception (combined right and left joint repositioning) improved 44.7% from pre- to post-training (p = 0.0006) and persisted (21.5%) for 9 months post-training. In addition there was a side interaction with the position sense of the right knee at 9 months showing 32.1% (p = 0.03) less deviation from the reference angle than the right knee during pre-testing. An instability-training program using Swiss balls with body weight as resistance can provide prolonged improvements in joint proprioception and core strength in previously untrained individuals performing this novel training stress which would contribute to general health.