Soil waterlogging in many arable regions of the world challenge the quantum and quality of crop production. While previous studies have assessed the impact of waterlogging on crop yields, understanding of how waterlogging implicates with crop quality remains in its infancy. Here, we conduct a systematic literature review and meta-analysis to assess how waterlogging influences grain quality. We also explore the role of engineering and agronomic strategies for alleviating adverse effects of waterlogging. We reveal that soil waterlogging has less impacts on grain quality than on yield; the latter decreasing by an average of 23 %, while average grain protein and starch content of waterlogged crops reduced by 6.7 % and 7.3 %, respectively. We attribute these differences to underlying mechanics of yield and grain quality formation, as well as biological processes conferring adaptation, plasticity and recovery. Reduced grain quality under waterlogging is associated with decreased activity of enzymes involved in leaf nitrogen and carbon metabolism. Unlike yields however, grain quality suffers less deterioration with prolonged waterlogging, with ultimate effects realized being a function of species-specific tolerance, timing and duration of waterlogging relative to crop stage, soil type and growing season weather. We underscore the potential in engineering and/or agronomic interventions for alleviating detrimental effects of waterlogging.