Evidence comparing ultrasound endoscopy-guided fine-needle biopsy (EUS-FNB) with EUS-guided fine-needle aspiration (EUS-FNA) in deep-seated lymphoma tissue sampling is insufficient. This study aims to evaluate the diagnostic efficacy of immunohistochemistry (IHC) or flow cytometry (FCM) on specimens obtained from EUS-FNB and EUS-FNA in the diagnosis and staging of deep-seated lymphomas. This real-world, dual-center study prospectively evaluated all eligible specimens from patients who underwent EUS-FNB/FNA over an 8-year period. 53 patients were enrolled, with 23 patients in the EUS-FNB group and 30 patients in the EUS-FNA group. FNB yielded specimens with longer core tissues (0.80 mm [0.55, 1.00] vs. 0.45 mm [0.30, 0.50], p = 0.009) and higher scores of specimen adequacy [4 (3.75, 4.00) vs. 3 (1.00, 4.00), p = 0.025]. Overall analysis revealed that the diagnostic accuracy of IHC based on specimens acquired from EUS-FNB was significantly higher than that of EUS-FNA (91.30% vs. 60.00%, p = 0.013). After controlling confounding factors including lesion size and endoscopists, EUS-FNB with IHC maintained a higher-level diagnostic accuracy compared to EUS-FNA (OR = 1.292 [1.037-1.609], p = 0.023). When FCM was additionally used to analyze the specimen acquired from EUS-FNA, the diagnostic yield was significantly improved (ROC AUC: 0.733 vs. 0.550, p = 0.015), and the AUC of FNB alone or combined with FCM was 0.739 and 0.761. Conclusions: FNB needles generate higher histopathological diagnostic accuracy and specimen quality than FNA for the deep-seated lymphoma. Though the application of FCM significantly improves the diagnostic efficacy of EUS-FNA, FNB was still the preferred diagnostic modality with a shorter procedure time, comparable diagnostic accuracy, and better cost-effectiveness.