Affine frequency division multiplexing (AFDM) has emerged as a promising waveform for high-mobility communications. However, its equalization remains a practical challenge under general physical channels with off-grid delay and Doppler effects. In this paper, we investigate frequency domain equalization for AFDM by considering a practical filtered-AFDM waveform. We analyze the input-output relations of filtered-AFDM across various domains and show that off-grid effects lead to severe inter-symbol interference in the DAFT domain, limiting the effectiveness of DAFT domain equalization. Motivated by the compactness of the frequency domain channel matrix in wideband systems, we propose a low-complexity two-stage frequency domain equalization scheme. Numerical results demonstrate that the proposed approach achieves performance close to full-block LMMSE equalization with significantly reduced computational complexity, and offers clear advantages over time domain equalization in wideband scenarios.