The use of living mulches (LM) grown in-season together with the cash crop is a potentially important method of organic vegetable production. There are only a few reports on the influence of LM on the biological value of vegetable crops. The impacts of LM of Alexandrian clover on the yields and levels of phenolic compounds in leeks and shallots were investigated. There were three sowing dates for the clover plants: 3 weeks before planting the leeks and shallot, at the planting date, and three weeks from planting the leeks and shallots. The yields of leeks and shallots with LM were higher than without the clover LM; the plants grown with LM accumulated more total phenolic (TP) compounds, and the plant extracts showed significantly higher antioxidant activity (AA). In shallot bulbs, the LM of Alexandrian clover increased the ferulic acid and chlorogenic acid levels, while in leek pseudo-stems the quercetin level was increased. The level of bioactive compounds depended on the date of clover planting. The most favorable sowing dates for clover planting were at the time of planting the leeks and shallots and three weeks after planting the plants. The LM of Alexandrian clover can be considered as a tool that can influence the nutritional value of leeks and shallots.