In Morocco, the citrus industry represents a lever for socio-economic growth at both regional and national levels. Despite numerous publications, existing reviews often treat biotic and abiotic stress types separately and address the use of endophytes as biostimulants for citrus plant growth and as bio-protectors for roots. The present work aims to highlight the interest in using fungal endophytes as a basis for developing inoculants to mitigate the effects of abiotic and biotic stresses. To achieve this objective, this review compiles and analyzes over a hundred published articles dealing with the problems of citrus farming in Morocco and the practices likely to optimize the processes of valorizing fungal endophytes, such as arbuscular mycorrhizal fungi (AMF) and filamentous fungi, or both in synergy. In this sense, this synthesis shows researchers that work on beneficial endophytes is still at the stage of isolation, identification, plant inoculation, and observation of the effect on various agronomic parameters. No endophyte-based inoculant has been formulated as a product that can be commercialized. Furthermore, to reach this stage, it is wise to clarify many points, such as the techniques for multiplying inoculants, formulation, preservation, and application. This information is necessary and offers perspectives to begin cycles of testing in the laboratory, greenhouse, and fields. These tests can form the basis for commercial formulations, based on endophytes, well-suited to Moroccan conditions, thereby offering better performance and greater resilience in the face of environmental challenges, notably drought and soil-borne diseases. They will present a significant opportunity to reduce dependence on imports and pave the way for greater aspirations for the citrus sector.