Capsules are widely used in bioengineering, chemical engineering and industry. The development of drug delivery systems using deformable capsules is progressing, yet the regulation of drug release within a capsule remains a challenge. Meanwhile, a microswimmer enclosed in a capsule can generate a large lubrication force on the capsule membrane, which could result in deformation and mechanical damage to the membrane. In this study, we numerically investigate how a capsule can be damaged by an enclosed microswimmer. The capsule membrane is modelled as a two-dimensional neo-Hookean material, with its deformability parametrised by capillary number. An isotropic brittle damage model is applied to express membrane rupture, with the Lighthill–Blake squirmer serving as the microswimmer model. In a sufficiently small capillary number regime, pusher-type squirmers exhibit stable swimming along the capsule membrane, while neutral-type and puller-type squirmers exhibit swimming towards the membrane and remain stationary. As capillary number increases, the damage to the membrane increases and rupture occurs in all swimming modes. For pusher-type squirmers, the critical capillary number leading to rupture is dependent on the initial incidence angle, whereas neutral-type and puller-type squirmers are independent of the initial value. Furthermore, we present methods for controlling membrane damage by magnetically orienting the microswimmer. The findings reveal that a static magnetic field can orient the microswimmer, leading to membrane damage and rupture even for a capsule that cannot be damaged by free swimming, while controlling the swimming path with a rotating magnetic field enables soft membranes to maintain deformation without rupture.