Quantum computing roadmaps predict the availability of 10,000 qubit devices within the next 3-5 years. With projected two-qubit error rates of 0.1%, these systems will enable certain operations under quantum error correction (QEC) using lightweight codes, offering significantly improved fidelities compared to the NISQ era. However, the high qubit cost of QEC codes like the surface code (especially at near-threshold physical error rates) limits the error correction capabilities of these devices. In this emerging era of Early Fault Tolerance (EFT), it will be essential to use QEC resources efficiently and focus on applications that derive the greatest benefit. In this work, we investigate the implementation of Variational Quantum Algorithms in the EFT regime (EFT-VQA). We introduce partial error correction (pQEC), a strategy that error-corrects Clifford operations while performing Rz rotations via magic state injection instead of the more expensive T-state distillation. Our results show that pQEC can improve VQA fidelities by 9.27x over standard approaches. Furthermore, we propose architectural optimizations that reduce circuit latency by ~2x, and achieve qubit packing efficiency of 66% in the EFT regime.