Understanding piezoelectricity, the linear electromechanical transduction, in bone and tendon and its potential role in mechanoelectric transduction leading to their growth and remodeling remains a challenging subject. With high-resolution piezoresponse force microscopy, we probed piezoelectric behavior in relevant biological samples at different scale levels: from the subfibrillar structures of single isolated collagen fibrils to bone. We revealed that, beyond the general understanding of collagen fibril being a piezoelectric material, there existed an intrinsic piezoelectric heterogeneity within a collagen fibril coinciding with the periodic variation of its gap and overlap regions. This piezoelectric heterogeneity persisted even for the collagen fibrils embedded in bone, bringing about new implications for its possible roles in structural formation and remodeling of bone.