After graduating, Northrop was commissioned as a second lieutenant of dragoons[3] and assigned to a series of posts, including duty in Florida Territory during the Second Seminole War.

The Southern economy was not organized for total war and did not possess the infrastructure required to generate large quantities of food, shoes, and clothing, nor to transport them for long distances.

In addition, severe inflation wracked the value of the Confederate currency that Northrop's men were authorized to offer to farms, shops, and small factories for goods desperately needed by the armies.

[5] Even when allowance is granted for factors beyond Colonel Northrop's control, however, his performance in supplying food, shoes, clothing, and other necessities to the armies of the Confederacy was judged inexcusably inadequate by historians such as Bell I. Wiley.

On numerous occasions, Confederate soldiers were forced to make do with scanty or inadequate rations, or to forage amongst their own countrymen for the necessities of life.

[5] As the war continued, Confederate soldiers began, in letters home and to their congressmen, to express concerns about the performance of the office of the Commissary-General.

Loyal to his friend, and aware of the overall logistical dilemmas facing the Confederacy, President Davis refrained from making Northrop into a scapegoat.

However, logistical problems worsened and reached a crescendo in the supply situation facing the Army of Northern Virginia during the Siege of Petersburg in the winter of 1864–1865.

Although Robert E. Lee's army had by this time become absolutely vital to the continued existence of the Confederacy, only two railroad lines (the Richmond & Danville and the Southside Railroad) linked the hungry soldiers with the fertile fields of Southside Virginia, and Northrop's commissary corps was pathetically unable to feed Lee's army.

Southern historian Bell I. Wiley, who specialized in examination of and research into the day-to-day experience of the combat troops of the American Civil War, grew to despise the tie between Davis and Northrop: A considerable factor in the President's unpopularity with Congress and with the country at large was his persistent support of discredited officials.