We present a subspace-based polynomial rooting algorithm to estimate the frequency bias (FB) of generalized frequency division multiplexing (GFDM) systems employing null subcarriers and repetitive sub-symbols. The estimation process is classified into fractional FB (FFB) and integer FB (IFB) estimation. The use of repetitive sub-symbols creates a quasi-periodic structure in the FB-distorted received signal, allowing the proposed algorithm to estimate the FFB using the root-MUSIC algorithm. Based on this, the proposed algorithm compensates for the FFB in the received signal and then estimates the null subcarrier pattern (NSP) in the frequency domain. As a result, the IFB estimate can be obtained in a maximum likelihood (ML) manner. Before the NSP estimation, this study uses a sub-symbol combiner to enhance signal strength of the FFB-aligned signal, ensuring the reliability of the IFB estimate. Computer simulations show that the proposed subspace-based algorithm has several advantages over traditional FB estimation methods: 1. Unlike some existing algorithms that use a training sequence to estimate FB, the proposed approach is a semi-blind algorithm because it can deliver information through repeated sub-symbols while estimating FB; 2. The proposed algorithm demonstrates excellent estimation accuracy compared to most traditional FB estimation algorithms; and 3. The proposed algorithm is computationally efficient, making it applicable to real-time applications in future communication systems.