1940s
| 1940 | Morgan |
| 1941 | Morgan |
| 1942 | Morgan |
| 1943 | Morgan |
| 1944 | Morgan |
| 1945 | Virginia State |
| 1946 | Morgan |
| 1947 | Shaw |
| 1948 | West Virginia State |
| 1949 | Morgan State |
1950s
| 1950 | NC A&T |
| 1951 | West Virginia State |
| 1952 | Virginia State |
| 1953 | NC College (NCCU) |
| 1954 | NC College (NCCU) |
| 1955 | Maryland State (Maryland-Eastern Shore) |
| 1956 | Maryland State, NC College, Delaware State (tie) |
| 1957 | Maryland State |
| 1958 | NC A&T |
| 1959 | NC A&T |
1960s
| 1960 | Maryland State |
| 1961 | NC College |
| 1962 | Morgan State |
| 1963 | NC College |
| 1964 | NC A&T |
| 1965 | Morgan State |
| 1966 | Morgan State |
| 1967 | Morgan State |
| 1968 | Morgan State |
| 1969 | Johnson C. Smith |
There are some inaccuracies in the championship count amongst institutions. Virginia State according to my count has 10. I couldn’t for the life of me find two more unless WVSU (two) were taken into account. Also you missed NCCU = 8, and VUU = 10
You also missed that Hampton had 13 Football Championships. In addition, the CIAA was founded on the campus of Hampton Institute (now Hampton University).