The management of cytologically indeterminate thyroid nodules remains debatable as their malignancy is difficult to establish. Most nodules have benign postoperative histology, but an accurate assessment of their proclivity for malignant transformation is crucial. Numerous studies have investigated the effects of various tools, including clinical, radiological, and cytological features, as well as biochemical and molecular markers, on the management of these heterogeneous nodules. Collectively, strategies aim to treat malignant nodules and avoid unnecessary surgery for asymptomatic benign nodules. Currently, no clear guidelines for the optimal management of cytologically indeterminate thyroid nodules exist to determine whether a conservative approach with long-term observation or surgical intervention should be selected. Thus, personalized approaches have been recommended. Large-scale multicenter prospective studies are needed to elucidate controversial issues. As this topic has not been comprehensively covered based on publications from the Gulf region, this review aims to shed light on remaining controversies.