In supervised quantum machine learning with classical data, classification performance critically depends on the geometry induced by quantum data embedding. Existing data-adaptive approaches rely on pairwise fidelity evaluations between samples, which scale as $O(B^2)$ for $B$ samples and create a computational bottleneck in iterative embedding optimization. To address this issue, we propose a prototype-guided framework for efficient data-adaptive quantum embedding. Using class-prototype separation and sample-to-prototype compactness, we derive a measurable lower certificate for class-ensemble distinguishability and construct a prototype-based objective requiring only $O(B)$ fidelity evaluations. We integrate this objective into an end-to-end pipeline that combines task-specific quantum circuit architecture optimization with continuous refinement of the data-embedding parameters. Across five benchmark datasets with up to 20 qubits, our method retains competitive quantum kernel support vector machine (SVM) performance while reducing fidelity-evaluation cost, with particularly strong gains over budget-matched pairwise optimization on T-MNIST. Geometric analyses examine how the learned embeddings relate to kernel alignment and classification margins, revealing dataset-dependent benefits and limitations. We further derive a prototype-based classifier in the reproducing kernel Hilbert space that provides an explicit witness for the SVM objective and a low-cost proxy for model selection, and extend the framework to multiple prototypes for multimodal class structures.

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