Traditional agricultural practices often result in gaseous losses of nitrous oxide (N2O), ammonia (NH3), and carbon dioxide (CO2), representing a net loss of nutrients from agricultural soils, which negatively impacts crop yield and requires farmers to increase nutrient inputs. By adopting best management practices (BMPs; i.e., no-tillage, cover crops, sub-surface manure application, and proper manure application timing), there is great potential to reduce these losses. Because N2O and CO2 are also greenhouse gases (GHGs), climate change mitigation via BMP adoption and emissions reductions would be an important co-benefit. However, adopting a no-tillage and cover cropping system has had setbacks within the Northeast, primarily due to concerns regarding manure nitrogen (N) losses in no-tillage systems as well as uncertainty surrounding the benefits of cover crops. This thesis used two field-trials located in Alburgh, Vermont to assess differences in (i) GHG emissions from agricultural soils, (ii) nitrate and ammonium retention, (iii) corn yield and protein content, and (iv) N uptake and retention via cover crop scavenging under a combination of different BMPs. Chapter 1 evaluates the effects of different reduced-tillage practices and manure application methods (i.e., vertical-tillage, no-tillage, manure injection, and broadcast manure application) on reducing N2O and CO2 emissions, retaining inorganic N, and improving crop yields. Greenhouse gas measurements were collected every other week for the growing season of 2015-2017 via static chamber method using a photoacoustic gas analyzer. Results from this study showed that tillage regimes and manure application method did not interact to affect any of the three research objectives, although differences between individual BMPs were observed. Notably, vertical tillage enhanced CO2 emissions relative to no-tillage, demonstrating the role of soil disturbance and aeration on aerobic microbial C transformations. Manure injection was found to significantly enhance both N2O and CO2 emission relative to broadcast application, likely due to the formation of anerobic micro-zones created from liquid manure injection. However, plots that received manure injection retained greater concentrations of soil nitrate, a vital nutrient for quality crop production, thereby highlighting a major tradeoff between gaseous N losses and N retention with manure injection. Chapter 2 evaluates the effects of tillage practices and timing of manure application to increase N retention with the use of cover crops in order to mitigate GHG emissions, enhance soil nitrate and ammonium retention, and improve cropping system N uptake. Treatments at this field trial consisted of a combination of the presence or absence of cover crops, no-tillage or conventional-tillage, and spring or fall manure application. Greenhouse gas emissions were measured every other week via static chamber method using a gas chromatograph for the growing season of 2018. Results from this study showed that the presence of cover crops enhanced both N2O and CO2 emissions relative to fallow land, irrespective of tillage regime and manure application season, likely as a result of greater N and carbon substrates entering the soil upon cover crop decomposition. Due to enhanced N2O emissions with cover crops, cover crops did not retain significantly greater inorganic N in the system upon termination.