Biocompatible functional materials play a significant role in drug delivery, tissue engineering and single cell analysis. We utilized 3D printing to produce high aspect ratio polymer resist microneedles on a silicon substrate and functionalized them by iron coating. Two-photon polymerization lithography has been used for printing cylindrical, pyramidal, and conical needles from a drop cast IP-DIP resist. Experiments with cells were conducted with cylindrical microneedles with 630 ± 15 nm in diameter with an aspect ratio of 1:10 and pitch of 12 μm. The needles have been arranged in square shaped arrays with various dimensions. The iron coating of the needles was 120 ± 15 nm thick and has isotropic magnetic behavior. The chemical composition and oxidation state were determined using energy electron loss spectroscopy, revealing a mixture of iron and Fe3O4 clusters. A biocompatibility assessment was performed through fluorescence microscopy using calcein/EthD-1 live/dead assay. The results show a very high biocompatibility of the iron coated needle arrays. This study provides a strategy to obtain electromagnetically functional microneedles that benefit from the flexibility in terms of geometry and shape of 3D printing. Potential applications are in areas like tissue engineering, single cell analysis or drug delivery.