One of the main limitations for future high-performance accelerators operating with positively charged particles is the formation of an electron-cloud inside the beam vacuum chamber, giving rise to instabilities. The Secondary Electron Yield (SEY) of the beam-facing surfaces gives a measure of the mechanism which drives this phenomenon. The laser-induced periodic structure formation on Cu surfaces has been demonstrated as a promising process to reduce SEY. In view of applications in beam chambers, we studied the laser process influence on SEY for 515 and 1030 nm wavelength femtosecond pulses on copper in different ambiences (air, nitrogen, vacuum). Depending on used process conditions, the surface composition differs, structures with varying aspect ratio are formed, i.e., periodic ripples and large-scale channels. Treatment in air at 515 nm is the most efficient for the formation of deeper structures allowing SEY maximum reduction first down to 1.6–1.7 and then below unity upon electron irradiation, thereby totally suppressing electron-cloud. Increasing the laser fluence, SEY will further reduce due to surface roughness enhancement via nanoparticle redeposition. This study reveals the fundamental role of LIPSS treatments to enable surface treatment in large-scale accelerator installations, where particle-free components are desired, and paves the way to potential future applications.