Monitoring electrical activity across multiple planes in 3D cell cultures and organoids is imperative to comprehensively understand their functional connections and behavior. However, traditional planar microelectrode arrays (MEAs) are intended for surface recordings and are inadequate in addressing this aspect. The limitations, such as longer production times and limited adaptability imposed by standard clean-room techniques, constrain the design possibilities for 3D electrode arrays and potentially hinder effective cell-electrode coupling. To tackle this challenge, a novel approach is presented that leverages rapid prototyping processes and additive manufacturing in combination with wet etching and electrodeposition to enhance electrode fabrication and performance. The laser-patterned MEAs on glass, polyimide (PI) foil, or polyethylene terephthalate (PET) foil substrates incorporate high-aspect ratio (up to 44:1) ink-jet printed 3D electrode structures with heights up to 1 mm at a pitch of 200 µm, enabling precise recording within cell tissues. The specific shapes of the electrode tips and customizable 3D structures provide great flexibility in electrode placement. The versatility of the 3D MEAs is demonstrated by recording the electrophysiological activity of cortical organoids in situ, paving the way for investigating neural activity under regular or various pathologically altered conditions in vitro in a high throughput manner.