Abstract Cover crops are grown between two main crops to reduce periods of bare fallow. In highly diverse crop rotations, the lengths of break periods between two main crops vary highly over time and consequently the cover cropping management differs from year to year. Long‐term field trials are thus of limited use because the same cover cropping approach only appears once in several years. This increases the need to better determine the immediate effects of different cover cropping strategies on soil properties. This study evaluated two cover cropping strategies and monitored the temporal development of several soil properties on six fields in Eastern Switzerland in the 9 months period between harvest of winter wheat and sowing of spring crops. The two tested strategies were (a) double cover cropping (DCC) where two cover crops mixtures were grown subsequently and shallowly (3 cm) incorporated into the topsoil and (b) permanent soil cover (PSC) with one grass‐clover mixture, which was harvested and thus not incorporated into the soil. Soil samples at three different soil depths (0–5, 5–10 and 10–20 cm) were sampled four times in high spatial resolution and analysed using a combined approach of visible near infrared spectroscopy and conventional lab methods. Differences between the sampling times and field sites were stronger than effects of different treatments. For soil organic carbon (SOC), no significant difference was measured between treatments in 0–20 cm soil depth. Only when analysed per depth segment, the PSC treatment showed significantly higher SOC increase in 5–10 cm soil depth than the DCC treatment. This could be due to the longer soil cover and thereby associated longer root growth period in the PSC treatment, leading to higher below ground C inputs than in the DCC treatment. On the other hand, the DCC treatment showed generally higher increases in permanganate oxidizable carbon stocks (0–5 cm), microbial C (0–10 cm), microbial N (0–10 cm) and mineral N (0–10 cm) than the PSC treatment. We conclude that maximizing cover crop above ground biomass input by planting two cover crops (DCC) benefitted soil microorganisms on most fields but was less beneficial on SOC than permanent soil cover (PSC) in 5–10 cm soil depth.