An imaging system such as an array camera may include an array of image sensors. The image sensors may each include an array of image pixels formed in a common image sensor substrate. A protective glass cover layer may be provided over the array of image sensors. The cover layer may be attached to the image sensor substrate using an adhesive. The adhesive may be formed on the image sensor substrate in a grid-like pattern in between adjacent image sensors in the array. A light blocking material may be formed on the adhesive grid to minimize optical crosstalk between neighboring image sensors. The light blocking material may fill or partially fill a trench in the adhesive, may coat the outer surfaces of the adhesive, and/or may coat the inner surfaces of the adhesive. If desired, light barriers may also be formed in openings in the glass cover layer.