Bessel beams (BBs) are propagation-invariant optical fields that retain a narrow central intensity profile over longer propagation lengths than Gaussian beams (GBs). Due to this property, they have been adopted in fluorescence-based light sheet microscopy (LSM) to obtain 2D longitudinally-extended light-sheets. Yet, current approaches for generating BB lattices in LSM focus on regular excitation patterns and involve complex and bulky optics, limiting integration capability and versatility. Here, a flexible method is presented to obtain BB-arrays with arbitrary geometries by encoding on a single sub-millimetric surface all the optical transformations required. This method is applied using a single metasurface to encode the generation of a linear array of BBs, avoiding the use of conjugation and focusing optics. With respect to the current strategies, this approach, allowing for the independent design of each beamlet of the array, increases the degrees of freedom while making optimal use of the available light with no rejection, thus facilitating its integration into optical systems. According to this method, we fabricated a metasurface-based optical element for generating a linear BB-array of excitation in an LSM configuration and recorded neuronal activity at cellular resolution from the zebrafish larva brain. Thus, the proposed approach greatly extends the BB-array versatility and the application scenarios.