Recently, consumers have demanded safe, nutritious, and healthy food. Due to rapid heat transfer, microwave treatment (MT) preserves nutritional quality and provides safe food. In this investigation, the effect of Microwave heating (MH) treatment was analysed on the bioactive components and quality characteristics of buransh (Rhododendron arboretum) flower squash. The fresh squash (TSS 19.6°Brix) was prepared by adjusting TSS to 3, 4, and 5°Brix by using RO water, and microwave treatment (MT) was given to the prepared squash as per the Box Behnken design (BBD). Process optimization was done using Design Expert 13 software. Microwave Power (MP), time, and total soluble solids (TSS) as process parameters showed significant (p < 0.05) effects on responses, namely pH, TSS, total phenolic content (TPC) and total flavonoid content (TFC). The optimized values at optimum process parameters (300 W, 30 s and 3°Brix) were found to be 3.79 for pH, 2.395°Brix for TSS, 44.28 mg GAE/100 mL for TPC and 132.159 mg QE/100 mL for TFC. The experimental values were found to be in accordance with the predicted values, having error (%) 0.5249, 3.96, 2.75, and 1.55 for pH, TSS, TPC, and TFC respectively. It was concluded that microwave heating can be used for the treatment of buransh (Rhododendron arboretum) flower squash with superior retention of nutritional quality.