Since the 1950s, plastic production has skyrocketed. Various environmental and human activities are leading to the formation and accumulation of microplastics (MPs) in aquatic and terrestrial ecosystems, causing detrimental effects on water, soil, plants, and living creatures. Wastewater treatment plants (WWTPs) are one of the primary MP management centers meant to check their entry into the natural systems. However, there are considerable limitations in effectively capturing, detecting, and characterizing these MPs in the inlet and outlet of WWTPs leading to “unaccounted MPs” that are eventually discharged into our ecosystems. In order to assess the holistic picture of the MPs’ distribution in the ecosystems, prevent the release of these omitted MPs into the environment, and formulate regulatory policies, it is vital to develop protocols that can be standardized across the globe to accurately detect and account for MPs in different sample types. This review will cover the details of current WWTP adoption procedures for MP management. Specifically, the following aspects are discussed: (i) several processes involved in the workflow of estimating MPs in the outlet of WWTPs; (ii) key limitations or challenges in each process that would increase the uncertainty in accurately estimating MPs; (iii) favorable recommendations that would lead to the standardization of protocols in the workflow and facilitate more accurate analysis of MPs; (iv) research opportunities to tackle the problem of ‘missing MPs’; and (v) future research directions for the efficient management of MPs. Considering the burgeoning research interest in the area of MPs, this work would help early scientists in understanding the current status in the field of MP analysis in the outlet of WWTPs.