In this work, we report a novel soft diffractive micro-optics, called ‘microscale kinoform phase-type lens (micro-KPL)’, which is fabricated by femtosecond laser direct writing (FsLDW) using bovine serum albumin (BSA) as building blocks and flexible polydimethylsiloxane (PDMS) slices as substrates. By carefully optimizing various process parameters of FsLDW (e.g., average laser power density, scanning step, exposure time on a single point and protein concentration), the as-formed protein micro-KPLs exhibit excellent surface quality, well-defined three-dimensional (3D) geometry and distinctive optical properties, even in relatively harsh operation environments (for instance, in strong acid or base). Laser shaping, imaging and other optical performances can be easily achieved. More importantly, micro-KPLs also have unique flexible and stretchable properties as well as good biocompatibility and biodegradability. Therefore, such protein hydrogel-based micro-optics may have great potential applications, such as in flexible and stretchable photonics and optics, soft integrated optical microsystems and bioimplantable devices.