In this dissertation, I focus on advanced manufacturing for multifunctional energy systems and functional materials in soft machines. In the first part of the dissertation, I introduce my effort in developing multifunctional energy systems for untethered underwater vehicles (UUVs) by showcasing the use of an aqueous battery for a high capacity jellyfish robot. In this part, I demonstrate the use of redox flow batteries (RFBs) configured to comply with shape, size, and mobility requirements associated with the jellyfish architecture with particular focus on two redox chemistries and architectures: (i) a secondary ZnBr2 battery with the highest areal capacity reported at a high current density, and (ii) a hybrid rechargeable primary ZnI2 battery with high capacity. For the first time, a UUV was able to be powered solely by RFB due to the increased power density demonstrated. The choice of a Jellyfish shape allows me to evaluate a low inertial moment robot architecture—a hemisphere, powered by batteries comprised primarily of liquids that are easily shaped to conform with the robot geometry. In our specific design, the RFB electrolyte also provides hydraulic force transmission to control the shape of the jellyfish’s bell, the dynamics of this shape change causes it to sink or swim. Finally, our choice of catholyte to fill the bell allows us to quickly recharge the battery by emptying the fluid and replacing it with pre-charged electrolyte (analogous to a gas station). In the second part of my dissertation, I describe our development of photo-ionic gels (PIGels) in ionotronics. The ability to control the movement of charged species in the circuitry of living beings and machines is essential for complex signal processing, computation, and, ultimately, higher functionality. We describe a class of photo-ion generators (PIGs) based on non-ionic photoacids that can create large (>1,000x) irreversible changes in ionic conductivity under illumination depending on the PIG species, concentration, and solvent. Incorporation of PIGs into polyurethane rubber by simple swelling methods yields soft (E >2 MPa) stretchable photo-ionic gels (PIGels), that can achieve a conductivity change of >300x. Meanwhile, the resolution of photopatterned conductivity in PIGels is less than 1 cm and demonstrates stability over several days, which suggests utility in engineered devices. Using this novel class of material, we demonstrate high sensitivity mechanical sensors via conductance changes ([∆G/G0]/σ = 20 MPa-1) and photo-writable soft circuitry.