We examine multidimensional polynomial progressions involving linearly independent polynomials in finite fields, proving power saving bounds for sets lacking such configurations. This jointly generalises earlier results of Peluse (for the single dimensional case) and the author (for distinct degree polynomials). In contrast to the cases studied in the aforementioned two papers, a usual PET induction argument does not give Gowers norm control over multidimensional progressions that involve polynomials of the same degrees. The main challenge is therefore to obtain Gowers norm control, and we accomplish this for all multidimensional polynomial progressions with pairwise independent polynomials. The key inputs are: (1) a quantitative version of a PET induction scheme developed in ergodic theory by Donoso, Koutsogiannis, Ferré-Moragues and Sun, (2) a quantitative concatenation result for Gowers box norms in arbitrary finite abelian groups, motivated by earlier results of Tao, Ziegler, Peluse and Prendiville; (3) an adaptation to combinatorics of the box norm smoothing technique, recently developed in the ergodic setting by the author and Frantzikinakis; and (4) a new version of the multidimensional degree lowering argument.