Phosphorus (P) is the main nutrient that causes eutrophication in fresh waters. The majority of P in lake ecosystems is usually stored in the bottom sediment, hence P cycling from the sediment into the water column can significantly and negatively impact water quality. However, sediment nutrients are not taken into account, for instance, in the ecological status assessment determined by the European Water Framework Directive. This encourages lake managers to improve the water quality at the expense of the sediment; for example, chemical inactivation of P has been applied to the sediment in numerous lakes for rapid water quality improvement. While this may generate immediate results, inactivation of sediment P may in fact delay the long-term recovery of lake ecosystems and inhibit the re-use of nutrients. In some specific cases, these rapid restoration efforts that compromise sediment quality are justified. Nevertheless, we should aim for a general strategy that can promote permanent recovery of lake ecosystems – including their sediments. The support for such restoration activities may be difficult to find, since the tangible outcome is realized only after long periods of time. Display omitted •Sediment nutrients are ignored in the ecological status assessment of lakes.•Many restoration methods improve water quality at the expense of the sediment.•Restoration methods that enrich sediment with P, delay long-term recovery of lakes.•P retained in lake sediments in restoration cannot be re-used.•More research should be targeted on restoration methods that remove P from lakes.