Background/Objectives: Benzodiazepine (BZD) withdrawal is frequently associated with altered emotional reactivity and behavior. Given the higher prevalence of anxiety disorders and the more frequent use of BZDs among women, understanding the neurobiology of BZD withdrawal in females is particularly important as it remains elusive. Methods: Adult female Wistar rats received 8 days of chronic, escalating-dose alprazolam (ALP) treatment followed by spontaneous withdrawal assessed at 36 h and 96 h from the last dose. Behavioral assessment was performed using the Open Field Test. Synaptic protein expression was analyzed by Western blot; neurotransmitter and neuromodulator levels were determined using high-performance liquid chromatography (HPLC) and commercial assay kits; and dendritic spine density and morphology were evaluated by Golgi–Cox staining. Results: ALP withdrawal significantly increased levels of anxiety-like behavior while reducing locomotor and exploratory activity. These behavioral changes were accompanied by increased glutamate levels and protein expression of vGluT1, GluR1, NR1, NR2B, and PSD-95, followed by delayed upregulation of EAAT1 and EAAT2. The GABAergic system exhibited heterogeneous remodeling, characterized by increased GAD65, α1-containing GABA_A receptors, and gephyrin, and reduced vGAT expression. Dopamine and serotonin levels remained unchanged, whereas D1 receptor levels were transiently reduced during 36 h withdrawal. The discontinuation of ALP was further associated with temporally selective dendritic spine remodeling, characterized by an early, sustained reduction in branched spine density, a transient increase in filopodia at 36 h, and a reduction in total spine density at 96 h. Conclusions: These findings demonstrate that ALP withdrawal leads to coordinated neurochemical, molecular, and structural remodeling within the amygdala, involving both excitatory and inhibitory synaptic compartments.