Low-intensity pulsed ultrasound (LIPUS) is a widely used non-invasive approach with therapeutic purposes since it provides physical stimulation with minimal thermal effects. The skin epithelium is the first barrier of the human body that interfaces with LIPUS and is subjected to the highest intensity. Little is known about the impact of LIPUS on the skin surface. This work investigates the biological effects of one-hour exposure to 1 MHz LIPUS on human keratinocytes HaCaT and tumoral SK-MEL-28 skin cells. Specifically, we evaluated the cellular state immediately after LIPUS treatment by analyzing cytogenetic endpoints and the response of cytoskeleton and cell junction proteins. Herein we demonstrate that LIPUS induces genomic damage as shown by an increase of chromosome malsegregation and a consequent decrease of cellular proliferation. The mechanical stimulus produced by LIPUS is also transmitted to the cytoskeletal compartment, inducing the expression and re-organization of junction proteins (i.e., E-cadherin and Desmosomes) and intermediate filaments (i.e., F-actin and Cytokeratins) with impact on cell morphology and cell adhesion. These in vitro results highlight the different outcomes following the cytogenetic damage and the resilience response exerted by the cytoskeleton upon mechanical stress, laying the foundation for future in vivo investigations.